Starting phenix.real_space_refine on Sun Mar 17 13:37:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdf_33146/03_2024/7xdf_33146_updated.pdb" } resolution = 2.72 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= 0.002 sd= 0.095 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 C 11396 2.51 5 N 3020 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17868 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.27, per 1000 atoms: 0.52 Number of scatterers: 17868 At special positions: 0 Unit cell: (77.9, 133.66, 133.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 16 15.00 O 3344 8.00 N 3020 7.00 C 11396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.07 Conformation dependent library (CDL) restraints added in 3.1 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 47.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 42 through 48 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.593A pdb=" N GLU A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 6.509A pdb=" N GLU A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.692A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.622A pdb=" N MET A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 179 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.937A pdb=" N CYS A 190 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 229 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.598A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.529A pdb=" N LEU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 516 through 536 removed outlier: 3.705A pdb=" N ILE A 519 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 521 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 524 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.569A pdb=" N ARG A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 42 through 48 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.594A pdb=" N GLU B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 removed outlier: 6.509A pdb=" N GLU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 143 through 149 removed outlier: 3.692A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 190 removed outlier: 3.622A pdb=" N MET B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 178 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 179 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 3.938A pdb=" N CYS B 190 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 229 through 246 Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.597A pdb=" N LYS B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 488 through 501 removed outlier: 3.529A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 516 through 536 removed outlier: 3.706A pdb=" N ILE B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 524 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.568A pdb=" N ARG B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 61 through 74 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.593A pdb=" N GLU C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 removed outlier: 6.508A pdb=" N GLU C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.692A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 190 removed outlier: 3.622A pdb=" N MET C 177 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 178 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 179 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 3.938A pdb=" N CYS C 190 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 229 through 246 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.598A pdb=" N LYS C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 377 through 384 Processing helix chain 'C' and resid 401 through 410 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 488 through 501 removed outlier: 3.529A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 516 through 536 removed outlier: 3.705A pdb=" N ILE C 519 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN C 520 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 521 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE C 524 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 556 removed outlier: 3.569A pdb=" N ARG C 556 " --> pdb=" O TYR C 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.594A pdb=" N GLU D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 removed outlier: 6.509A pdb=" N GLU D 105 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.692A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 190 removed outlier: 3.622A pdb=" N MET D 177 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY D 178 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 179 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 3.939A pdb=" N CYS D 190 " --> pdb=" O TYR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 229 through 246 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.597A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 401 through 410 Processing helix chain 'D' and resid 430 through 436 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 488 through 501 removed outlier: 3.529A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 516 through 536 removed outlier: 3.705A pdb=" N ILE D 519 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN D 520 " --> pdb=" O ALA D 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 521 " --> pdb=" O ASN D 518 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 524 " --> pdb=" O GLU D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 556 removed outlier: 3.567A pdb=" N ARG D 556 " --> pdb=" O TYR D 552 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.757A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 251 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 160 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A 253 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE A 344 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 309 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 388 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 310 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 390 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 415 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 391 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 417 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 442 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA A 418 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 444 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.756A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 251 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 160 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN B 253 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE B 344 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 309 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR B 388 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 310 " --> pdb=" O THR B 388 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 390 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 415 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY B 391 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 417 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU B 442 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA B 418 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B 444 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.756A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 251 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL C 160 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN C 253 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 344 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE C 309 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 388 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 310 " --> pdb=" O THR C 388 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 390 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 415 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY C 391 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE C 417 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU C 442 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA C 418 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA C 444 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.758A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 251 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 160 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN D 253 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 344 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 309 " --> pdb=" O PHE D 344 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 388 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 310 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 390 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 415 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY D 391 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 417 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU D 442 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA D 418 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA D 444 " --> pdb=" O ALA D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 584 hydrogen bonds defined for protein. 1440 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: 5.13 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2948 1.31 - 1.43: 4782 1.43 - 1.56: 10338 1.56 - 1.68: 72 1.68 - 1.81: 148 Bond restraints: 18288 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.230 0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD C 602 " pdb=" C3D NAD C 602 " ideal model delta sigma weight residual 1.531 1.237 0.294 2.00e-02 2.50e+03 2.16e+02 ... (remaining 18283 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.75: 411 104.75 - 112.07: 9093 112.07 - 119.38: 5667 119.38 - 126.70: 9449 126.70 - 134.01: 224 Bond angle restraints: 24844 Sorted by residual: angle pdb=" O1A NAD B 602 " pdb=" PA NAD B 602 " pdb=" O2A NAD B 602 " ideal model delta sigma weight residual 122.64 109.25 13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD C 602 " pdb=" PA NAD C 602 " pdb=" O2A NAD C 602 " ideal model delta sigma weight residual 122.64 109.26 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 109.28 13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 ... (remaining 24839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 10040 17.13 - 34.27: 976 34.27 - 51.40: 157 51.40 - 68.53: 69 68.53 - 85.67: 38 Dihedral angle restraints: 11280 sinusoidal: 4896 harmonic: 6384 Sorted by residual: dihedral pdb=" CA GLU C 304 " pdb=" C GLU C 304 " pdb=" N HIS C 305 " pdb=" CA HIS C 305 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU B 304 " pdb=" C GLU B 304 " pdb=" N HIS B 305 " pdb=" CA HIS B 305 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N HIS A 305 " pdb=" CA HIS A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 11277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2445 0.075 - 0.151: 257 0.151 - 0.226: 22 0.226 - 0.302: 4 0.302 - 0.377: 4 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C4D NAD B 601 " pdb=" C3D NAD B 601 " pdb=" C5D NAD B 601 " pdb=" O4D NAD B 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C4D NAD C 601 " pdb=" C3D NAD C 601 " pdb=" C5D NAD C 601 " pdb=" O4D NAD C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C4D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" C5D NAD A 601 " pdb=" O4D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2729 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 26 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO B 27 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 26 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO C 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 26 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.027 5.00e-02 4.00e+02 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 266 2.63 - 3.20: 16637 3.20 - 3.77: 28116 3.77 - 4.33: 41328 4.33 - 4.90: 68013 Nonbonded interactions: 154360 Sorted by model distance: nonbonded pdb=" OD1 ASP A 236 " pdb=" OH TYR A 269 " model vdw 2.065 2.440 nonbonded pdb=" OD1 ASP C 236 " pdb=" OH TYR C 269 " model vdw 2.065 2.440 nonbonded pdb=" OD1 ASP B 236 " pdb=" OH TYR B 269 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASP D 236 " pdb=" OH TYR D 269 " model vdw 2.066 2.440 nonbonded pdb=" OE2 GLU B 59 " pdb=" NH2 ARG B 67 " model vdw 2.089 2.520 ... (remaining 154355 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 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: 3.150 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: 0.020 Extract box with map and model: 12.600 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 47.260 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.014 0.301 18288 Z= 0.906 Angle : 0.929 13.390 24844 Z= 0.432 Chirality : 0.049 0.377 2732 Planarity : 0.006 0.048 3164 Dihedral : 14.801 85.667 7192 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.28 (0.17), residues: 2196 helix: 0.35 (0.16), residues: 1036 sheet: 1.03 (0.36), residues: 204 loop : -0.02 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS C 305 PHE 0.023 0.002 PHE D 471 TYR 0.013 0.001 TYR B 562 ARG 0.012 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.019 Fit side-chains REVERT: A 152 GLU cc_start: 0.7477 (mp0) cc_final: 0.7190 (tp30) REVERT: A 314 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 334 GLU cc_start: 0.7586 (tt0) cc_final: 0.7342 (tt0) REVERT: A 352 LYS cc_start: 0.5859 (mmpt) cc_final: 0.4650 (pttt) REVERT: A 359 ASP cc_start: 0.7526 (m-30) cc_final: 0.7264 (m-30) REVERT: A 398 LEU cc_start: 0.7420 (mm) cc_final: 0.7190 (mm) REVERT: A 460 PHE cc_start: 0.7819 (m-80) cc_final: 0.7421 (m-80) REVERT: A 488 ASP cc_start: 0.7397 (m-30) cc_final: 0.6964 (m-30) REVERT: A 565 LEU cc_start: 0.9033 (mt) cc_final: 0.8826 (mt) REVERT: B 29 MET cc_start: 0.8452 (mtp) cc_final: 0.8226 (mtp) REVERT: B 152 GLU cc_start: 0.7508 (mp0) cc_final: 0.7229 (tp30) REVERT: B 352 LYS cc_start: 0.5974 (mmpt) cc_final: 0.4766 (pttt) REVERT: B 359 ASP cc_start: 0.7523 (m-30) cc_final: 0.7279 (m-30) REVERT: B 460 PHE cc_start: 0.7770 (m-80) cc_final: 0.7390 (m-80) REVERT: B 488 ASP cc_start: 0.7374 (m-30) cc_final: 0.6958 (m-30) REVERT: C 29 MET cc_start: 0.8447 (mtp) cc_final: 0.8219 (mtp) REVERT: C 152 GLU cc_start: 0.7519 (mp0) cc_final: 0.7222 (tp30) REVERT: C 210 ILE cc_start: 0.8340 (pt) cc_final: 0.8138 (tp) REVERT: C 314 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 352 LYS cc_start: 0.5933 (mmpt) cc_final: 0.4693 (pttt) REVERT: C 359 ASP cc_start: 0.7511 (m-30) cc_final: 0.7248 (m-30) REVERT: C 398 LEU cc_start: 0.7400 (mm) cc_final: 0.7180 (mm) REVERT: C 460 PHE cc_start: 0.7804 (m-80) cc_final: 0.7423 (m-80) REVERT: C 488 ASP cc_start: 0.7375 (m-30) cc_final: 0.6959 (m-30) REVERT: C 565 LEU cc_start: 0.9038 (mt) cc_final: 0.8835 (mt) REVERT: D 29 MET cc_start: 0.8408 (mtp) cc_final: 0.8176 (mtp) REVERT: D 152 GLU cc_start: 0.7472 (mp0) cc_final: 0.7205 (tp30) REVERT: D 314 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6758 (mm-30) REVERT: D 334 GLU cc_start: 0.7582 (tt0) cc_final: 0.7337 (tt0) REVERT: D 352 LYS cc_start: 0.5939 (mmpt) cc_final: 0.4717 (pttt) REVERT: D 359 ASP cc_start: 0.7540 (m-30) cc_final: 0.7291 (m-30) REVERT: D 398 LEU cc_start: 0.7419 (mm) cc_final: 0.7210 (mm) REVERT: D 460 PHE cc_start: 0.7805 (m-80) cc_final: 0.7400 (m-80) REVERT: D 488 ASP cc_start: 0.7377 (m-30) cc_final: 0.6948 (m-30) REVERT: D 565 LEU cc_start: 0.9039 (mt) cc_final: 0.8830 (mt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 1.3583 time to fit residues: 510.4890 Evaluate side-chains 229 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 425 GLN A 501 GLN A 509 GLN B 61 GLN B 425 GLN B 501 GLN C 425 GLN C 501 GLN D 425 GLN D 501 GLN D 509 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18288 Z= 0.192 Angle : 0.546 6.007 24844 Z= 0.276 Chirality : 0.043 0.187 2732 Planarity : 0.005 0.044 3164 Dihedral : 10.784 59.079 2908 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.71 % Allowed : 9.15 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.57 (0.18), residues: 2196 helix: 0.63 (0.16), residues: 1048 sheet: 1.13 (0.36), residues: 204 loop : 0.08 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.006 0.001 HIS A 305 PHE 0.022 0.002 PHE B 471 TYR 0.009 0.001 TYR B 469 ARG 0.002 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 222 time to evaluate : 2.148 Fit side-chains REVERT: A 105 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: A 118 LEU cc_start: 0.7950 (tp) cc_final: 0.7639 (mt) REVERT: A 314 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6658 (mm-30) REVERT: A 334 GLU cc_start: 0.7557 (tt0) cc_final: 0.7315 (tt0) REVERT: A 352 LYS cc_start: 0.6005 (mmpt) cc_final: 0.4795 (pttt) REVERT: A 359 ASP cc_start: 0.7529 (m-30) cc_final: 0.7293 (m-30) REVERT: A 488 ASP cc_start: 0.7328 (m-30) cc_final: 0.7037 (m-30) REVERT: B 105 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 118 LEU cc_start: 0.7973 (tp) cc_final: 0.7621 (mp) REVERT: B 352 LYS cc_start: 0.6152 (mmpt) cc_final: 0.4928 (pttt) REVERT: B 359 ASP cc_start: 0.7555 (m-30) cc_final: 0.7318 (m-30) REVERT: B 488 ASP cc_start: 0.7337 (m-30) cc_final: 0.7050 (m-30) REVERT: C 105 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: C 118 LEU cc_start: 0.7966 (tp) cc_final: 0.7630 (mt) REVERT: C 314 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6655 (mm-30) REVERT: C 352 LYS cc_start: 0.6100 (mmpt) cc_final: 0.4873 (pttt) REVERT: C 359 ASP cc_start: 0.7571 (m-30) cc_final: 0.7315 (m-30) REVERT: C 405 ARG cc_start: 0.6414 (ptp90) cc_final: 0.5697 (mtt90) REVERT: C 488 ASP cc_start: 0.7351 (m-30) cc_final: 0.7065 (m-30) REVERT: D 105 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: D 118 LEU cc_start: 0.7941 (tp) cc_final: 0.7622 (mt) REVERT: D 314 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6667 (mm-30) REVERT: D 334 GLU cc_start: 0.7565 (tt0) cc_final: 0.7327 (tt0) REVERT: D 352 LYS cc_start: 0.5981 (mmpt) cc_final: 0.4806 (pttt) REVERT: D 359 ASP cc_start: 0.7544 (m-30) cc_final: 0.7300 (m-30) REVERT: D 363 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6925 (tm-30) REVERT: D 488 ASP cc_start: 0.7327 (m-30) cc_final: 0.7041 (m-30) outliers start: 32 outliers final: 8 residues processed: 249 average time/residue: 1.4242 time to fit residues: 393.9903 Evaluate side-chains 226 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 216 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN A 509 GLN B 425 GLN C 61 GLN C 425 GLN D 61 GLN D 425 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18288 Z= 0.182 Angle : 0.515 5.758 24844 Z= 0.259 Chirality : 0.043 0.196 2732 Planarity : 0.005 0.040 3164 Dihedral : 8.739 55.228 2908 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.93 % Allowed : 10.81 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.67 (0.18), residues: 2196 helix: 0.72 (0.16), residues: 1052 sheet: 1.03 (0.35), residues: 204 loop : 0.16 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 558 HIS 0.006 0.001 HIS A 305 PHE 0.020 0.002 PHE A 471 TYR 0.009 0.001 TYR C 469 ARG 0.003 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7671 (mt) REVERT: A 334 GLU cc_start: 0.7564 (tt0) cc_final: 0.7348 (tt0) REVERT: A 352 LYS cc_start: 0.6108 (mmpt) cc_final: 0.4880 (pttt) REVERT: A 359 ASP cc_start: 0.7578 (m-30) cc_final: 0.7338 (m-30) REVERT: A 405 ARG cc_start: 0.7171 (mtp85) cc_final: 0.6365 (mtt90) REVERT: B 118 LEU cc_start: 0.7956 (tp) cc_final: 0.7755 (mt) REVERT: B 352 LYS cc_start: 0.6138 (mmpt) cc_final: 0.4890 (pttt) REVERT: B 359 ASP cc_start: 0.7647 (m-30) cc_final: 0.7432 (m-30) REVERT: B 488 ASP cc_start: 0.7332 (m-30) cc_final: 0.7128 (m-30) REVERT: C 118 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7664 (mt) REVERT: C 210 ILE cc_start: 0.8318 (pp) cc_final: 0.8023 (pt) REVERT: C 352 LYS cc_start: 0.6109 (mmpt) cc_final: 0.4869 (pttt) REVERT: C 359 ASP cc_start: 0.7583 (m-30) cc_final: 0.7348 (m-30) REVERT: C 373 ILE cc_start: 0.7235 (tp) cc_final: 0.6771 (pt) REVERT: C 488 ASP cc_start: 0.7336 (m-30) cc_final: 0.7132 (m-30) REVERT: D 118 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (mt) REVERT: D 334 GLU cc_start: 0.7578 (tt0) cc_final: 0.7366 (tt0) REVERT: D 352 LYS cc_start: 0.6069 (mmpt) cc_final: 0.4930 (pttt) REVERT: D 359 ASP cc_start: 0.7597 (m-30) cc_final: 0.7363 (m-30) REVERT: D 563 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7733 (p0) outliers start: 36 outliers final: 9 residues processed: 239 average time/residue: 1.3440 time to fit residues: 359.1776 Evaluate side-chains 199 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 563 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18288 Z= 0.187 Angle : 0.507 5.794 24844 Z= 0.255 Chirality : 0.042 0.207 2732 Planarity : 0.005 0.040 3164 Dihedral : 8.116 55.457 2908 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.66 % Allowed : 12.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.69 (0.18), residues: 2196 helix: 0.77 (0.16), residues: 1056 sheet: 0.55 (0.31), residues: 256 loop : 0.25 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.005 0.001 HIS A 305 PHE 0.019 0.001 PHE A 471 TYR 0.008 0.001 TYR B 469 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7554 (tt0) cc_final: 0.7346 (tt0) REVERT: A 335 GLN cc_start: 0.7114 (tp40) cc_final: 0.6840 (mp10) REVERT: A 352 LYS cc_start: 0.6104 (mmpt) cc_final: 0.4913 (pttt) REVERT: A 359 ASP cc_start: 0.7611 (m-30) cc_final: 0.7371 (m-30) REVERT: A 405 ARG cc_start: 0.7161 (mtp85) cc_final: 0.6345 (mtt90) REVERT: B 335 GLN cc_start: 0.7199 (tp40) cc_final: 0.6902 (mp10) REVERT: B 352 LYS cc_start: 0.6134 (mmpt) cc_final: 0.4921 (pttt) REVERT: B 359 ASP cc_start: 0.7589 (m-30) cc_final: 0.7384 (m-30) REVERT: B 488 ASP cc_start: 0.7381 (m-30) cc_final: 0.7124 (m-30) REVERT: C 335 GLN cc_start: 0.7208 (tp40) cc_final: 0.6893 (mp10) REVERT: C 352 LYS cc_start: 0.6095 (mmpt) cc_final: 0.4871 (pttt) REVERT: C 359 ASP cc_start: 0.7587 (m-30) cc_final: 0.7364 (m-30) REVERT: C 488 ASP cc_start: 0.7376 (m-30) cc_final: 0.7119 (m-30) REVERT: D 334 GLU cc_start: 0.7554 (tt0) cc_final: 0.7347 (tt0) REVERT: D 335 GLN cc_start: 0.7122 (tp40) cc_final: 0.6842 (mp10) REVERT: D 352 LYS cc_start: 0.6088 (mmpt) cc_final: 0.4945 (pttt) REVERT: D 359 ASP cc_start: 0.7584 (m-30) cc_final: 0.7343 (m-30) outliers start: 31 outliers final: 10 residues processed: 231 average time/residue: 1.3544 time to fit residues: 349.3159 Evaluate side-chains 197 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 181 optimal weight: 0.0070 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18288 Z= 0.264 Angle : 0.540 5.928 24844 Z= 0.273 Chirality : 0.044 0.193 2732 Planarity : 0.005 0.040 3164 Dihedral : 8.572 58.327 2908 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.93 % Allowed : 13.01 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.56 (0.17), residues: 2196 helix: 0.65 (0.16), residues: 1060 sheet: 0.45 (0.31), residues: 256 loop : 0.21 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 558 HIS 0.006 0.001 HIS D 305 PHE 0.023 0.002 PHE A 471 TYR 0.012 0.001 TYR A 97 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7554 (tt0) cc_final: 0.7315 (tt0) REVERT: A 335 GLN cc_start: 0.7118 (tp40) cc_final: 0.6827 (mp10) REVERT: A 352 LYS cc_start: 0.6089 (mmpt) cc_final: 0.4909 (pttt) REVERT: A 359 ASP cc_start: 0.7658 (m-30) cc_final: 0.7455 (m-30) REVERT: A 405 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6339 (mtt90) REVERT: A 438 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: B 335 GLN cc_start: 0.7260 (tp40) cc_final: 0.6922 (mp10) REVERT: B 352 LYS cc_start: 0.6161 (mmpt) cc_final: 0.4984 (pttt) REVERT: B 438 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6438 (pt0) REVERT: B 488 ASP cc_start: 0.7398 (m-30) cc_final: 0.7140 (m-30) REVERT: C 335 GLN cc_start: 0.7234 (tp40) cc_final: 0.6897 (mp10) REVERT: C 352 LYS cc_start: 0.6119 (mmpt) cc_final: 0.4921 (pttt) REVERT: C 488 ASP cc_start: 0.7401 (m-30) cc_final: 0.7136 (m-30) REVERT: D 335 GLN cc_start: 0.7153 (tp40) cc_final: 0.6853 (mp10) REVERT: D 352 LYS cc_start: 0.6124 (mmpt) cc_final: 0.4950 (pttt) REVERT: D 359 ASP cc_start: 0.7702 (m-30) cc_final: 0.7483 (m-30) outliers start: 36 outliers final: 18 residues processed: 226 average time/residue: 1.3612 time to fit residues: 344.2542 Evaluate side-chains 207 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 295 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 212 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 98 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18288 Z= 0.179 Angle : 0.503 5.747 24844 Z= 0.253 Chirality : 0.042 0.180 2732 Planarity : 0.004 0.039 3164 Dihedral : 8.158 59.960 2908 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.61 % Allowed : 14.45 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.18), residues: 2196 helix: 0.77 (0.16), residues: 1056 sheet: 0.38 (0.31), residues: 256 loop : 0.20 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 PHE 0.018 0.001 PHE A 471 TYR 0.007 0.001 TYR C 469 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7530 (tt0) cc_final: 0.7298 (tt0) REVERT: A 352 LYS cc_start: 0.6121 (mmpt) cc_final: 0.4947 (pttt) REVERT: A 405 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6362 (mtt180) REVERT: A 438 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: B 335 GLN cc_start: 0.7260 (tp40) cc_final: 0.6894 (mp10) REVERT: B 352 LYS cc_start: 0.6176 (mmpt) cc_final: 0.5045 (pttt) REVERT: B 488 ASP cc_start: 0.7399 (m-30) cc_final: 0.7146 (m-30) REVERT: B 501 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: C 335 GLN cc_start: 0.7245 (tp40) cc_final: 0.6975 (mp10) REVERT: C 352 LYS cc_start: 0.6146 (mmpt) cc_final: 0.5012 (pttt) REVERT: C 501 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: D 335 GLN cc_start: 0.7201 (tp40) cc_final: 0.6846 (mp10) REVERT: D 352 LYS cc_start: 0.6110 (mmpt) cc_final: 0.4897 (pttt) REVERT: D 359 ASP cc_start: 0.7698 (m-30) cc_final: 0.7485 (m-30) outliers start: 30 outliers final: 15 residues processed: 211 average time/residue: 1.3756 time to fit residues: 323.9954 Evaluate side-chains 200 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18288 Z= 0.180 Angle : 0.495 5.788 24844 Z= 0.249 Chirality : 0.042 0.180 2732 Planarity : 0.004 0.038 3164 Dihedral : 7.507 57.241 2908 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.14 % Allowed : 14.29 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.67 (0.18), residues: 2196 helix: 0.88 (0.16), residues: 1032 sheet: 0.40 (0.31), residues: 256 loop : 0.12 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.005 0.001 HIS A 305 PHE 0.019 0.001 PHE A 471 TYR 0.007 0.001 TYR C 469 ARG 0.003 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7524 (tt0) cc_final: 0.7314 (tt0) REVERT: A 352 LYS cc_start: 0.6176 (mmpt) cc_final: 0.4982 (pptt) REVERT: A 405 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6336 (mtt180) REVERT: A 438 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6195 (pm20) REVERT: B 335 GLN cc_start: 0.7251 (tp40) cc_final: 0.6879 (mp10) REVERT: B 352 LYS cc_start: 0.6218 (mmpt) cc_final: 0.5007 (pptt) REVERT: B 501 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: C 335 GLN cc_start: 0.7261 (tp40) cc_final: 0.6883 (mp10) REVERT: C 352 LYS cc_start: 0.6220 (mmpt) cc_final: 0.5004 (pptt) REVERT: C 501 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: D 335 GLN cc_start: 0.7182 (tp40) cc_final: 0.6845 (mp10) REVERT: D 352 LYS cc_start: 0.6090 (mmpt) cc_final: 0.4960 (pttt) outliers start: 40 outliers final: 26 residues processed: 227 average time/residue: 1.3171 time to fit residues: 334.5103 Evaluate side-chains 211 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN B 92 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN D 92 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18288 Z= 0.167 Angle : 0.485 5.824 24844 Z= 0.245 Chirality : 0.041 0.178 2732 Planarity : 0.004 0.039 3164 Dihedral : 7.159 55.769 2908 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.87 % Allowed : 14.51 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2196 helix: 0.97 (0.16), residues: 1028 sheet: 0.45 (0.32), residues: 256 loop : 0.18 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 558 HIS 0.005 0.001 HIS A 305 PHE 0.018 0.001 PHE D 471 TYR 0.006 0.001 TYR C 469 ARG 0.005 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 2.174 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: A 339 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7372 (mmmm) REVERT: A 352 LYS cc_start: 0.6200 (mmpt) cc_final: 0.5028 (pptt) REVERT: A 438 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6087 (pm20) REVERT: B 335 GLN cc_start: 0.7299 (tp40) cc_final: 0.6831 (mp10) REVERT: B 339 LYS cc_start: 0.7733 (mmtp) cc_final: 0.7341 (mmmm) REVERT: B 352 LYS cc_start: 0.6249 (mmpt) cc_final: 0.5079 (pptt) REVERT: C 335 GLN cc_start: 0.7266 (tp40) cc_final: 0.6813 (mp10) REVERT: C 339 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7343 (mmmm) REVERT: C 352 LYS cc_start: 0.6210 (mmpt) cc_final: 0.5021 (pptt) REVERT: C 438 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6378 (pt0) REVERT: D 335 GLN cc_start: 0.7328 (tp40) cc_final: 0.6853 (mp10) REVERT: D 339 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7339 (mmmm) REVERT: D 352 LYS cc_start: 0.6102 (mmpt) cc_final: 0.4964 (pttt) REVERT: D 438 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6341 (pt0) outliers start: 35 outliers final: 26 residues processed: 219 average time/residue: 1.3316 time to fit residues: 327.2858 Evaluate side-chains 210 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 178 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 GLN D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18288 Z= 0.167 Angle : 0.487 5.874 24844 Z= 0.245 Chirality : 0.042 0.186 2732 Planarity : 0.004 0.039 3164 Dihedral : 7.008 55.083 2908 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.09 % Allowed : 14.45 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.80 (0.18), residues: 2196 helix: 1.01 (0.16), residues: 1028 sheet: 0.50 (0.32), residues: 256 loop : 0.16 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.005 0.001 HIS D 305 PHE 0.019 0.001 PHE D 471 TYR 0.006 0.001 TYR C 469 ARG 0.004 0.000 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.976 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: A 339 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7370 (mmmm) REVERT: A 352 LYS cc_start: 0.6189 (mmpt) cc_final: 0.5045 (pptt) REVERT: B 335 GLN cc_start: 0.7315 (tp40) cc_final: 0.6834 (mp10) REVERT: B 339 LYS cc_start: 0.7722 (mmtp) cc_final: 0.7337 (mmmm) REVERT: B 352 LYS cc_start: 0.6268 (mmpt) cc_final: 0.5098 (pptt) REVERT: B 438 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6339 (pt0) REVERT: C 335 GLN cc_start: 0.7303 (tp40) cc_final: 0.6818 (mp10) REVERT: C 339 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7341 (mmmm) REVERT: C 352 LYS cc_start: 0.6199 (mmpt) cc_final: 0.5043 (pptt) REVERT: C 438 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: D 335 GLN cc_start: 0.7292 (tp40) cc_final: 0.6819 (mp10) REVERT: D 339 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7368 (mmmm) REVERT: D 352 LYS cc_start: 0.6111 (mmpt) cc_final: 0.4968 (pttt) REVERT: D 438 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6356 (pt0) outliers start: 39 outliers final: 32 residues processed: 218 average time/residue: 1.3206 time to fit residues: 323.1685 Evaluate side-chains 212 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0670 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18288 Z= 0.174 Angle : 0.489 5.867 24844 Z= 0.247 Chirality : 0.042 0.188 2732 Planarity : 0.004 0.039 3164 Dihedral : 6.944 55.513 2908 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.93 % Allowed : 14.61 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.83 (0.18), residues: 2196 helix: 1.04 (0.17), residues: 1020 sheet: 0.51 (0.32), residues: 256 loop : 0.16 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 558 HIS 0.005 0.001 HIS B 305 PHE 0.020 0.001 PHE D 471 TYR 0.007 0.001 TYR A 469 ARG 0.003 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.937 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: A 339 LYS cc_start: 0.7742 (mmtp) cc_final: 0.7367 (mmmm) REVERT: A 352 LYS cc_start: 0.6163 (mmpt) cc_final: 0.5020 (pptt) REVERT: A 405 ARG cc_start: 0.6749 (mtp-110) cc_final: 0.6062 (mtt180) REVERT: B 335 GLN cc_start: 0.7300 (tp40) cc_final: 0.6804 (mp10) REVERT: B 339 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7350 (mmmm) REVERT: B 352 LYS cc_start: 0.6267 (mmpt) cc_final: 0.5117 (pptt) REVERT: C 335 GLN cc_start: 0.7301 (tp40) cc_final: 0.6802 (mp10) REVERT: C 339 LYS cc_start: 0.7768 (mmtp) cc_final: 0.7372 (mmmm) REVERT: C 352 LYS cc_start: 0.6202 (mmpt) cc_final: 0.5056 (pptt) REVERT: D 335 GLN cc_start: 0.7297 (tp40) cc_final: 0.6800 (mp10) REVERT: D 339 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7391 (mmmm) REVERT: D 352 LYS cc_start: 0.6161 (mmpt) cc_final: 0.4936 (pttt) outliers start: 36 outliers final: 32 residues processed: 216 average time/residue: 1.2793 time to fit residues: 310.4104 Evaluate side-chains 210 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 295 GLN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 174 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106327 restraints weight = 20914.179| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.88 r_work: 0.3159 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18288 Z= 0.190 Angle : 0.500 5.902 24844 Z= 0.252 Chirality : 0.042 0.193 2732 Planarity : 0.004 0.038 3164 Dihedral : 6.980 56.522 2908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.82 % Allowed : 14.72 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.81 (0.18), residues: 2196 helix: 1.00 (0.17), residues: 1024 sheet: 0.51 (0.32), residues: 256 loop : 0.17 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.005 0.001 HIS C 305 PHE 0.021 0.001 PHE D 471 TYR 0.008 0.001 TYR B 97 ARG 0.003 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.93 seconds wall clock time: 113 minutes 26.46 seconds (6806.46 seconds total)