Starting phenix.real_space_refine on Sat Feb 17 19:31:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekr_28211/02_2024/8ekr_28211_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 4 5.49 5 S 112 5.16 5 C 12940 2.51 5 N 3288 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 305": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.68, per 1000 atoms: 0.54 Number of scatterers: 19712 At special positions: 0 Unit cell: (137.97, 137.97, 113.15, 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 112 16.00 P 4 15.00 O 3368 8.00 N 3288 7.00 C 12940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.7 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 4 sheets defined 53.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.075A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.587A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 309 through 315 removed outlier: 3.754A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 378 through 413 removed outlier: 5.247A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 460 through 465 removed outlier: 4.534A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 removed outlier: 4.046A pdb=" N ALA A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 518 removed outlier: 4.020A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.527A pdb=" N LEU A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 514 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 558 Processing helix chain 'A' and resid 593 through 603 removed outlier: 4.339A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 649 Processing helix chain 'A' and resid 656 through 673 removed outlier: 3.975A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.075A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.587A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 309 through 315 removed outlier: 3.754A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 413 removed outlier: 5.247A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 460 through 465 removed outlier: 4.536A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 491 removed outlier: 4.047A pdb=" N ALA B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 518 removed outlier: 4.021A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.527A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 514 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 removed outlier: 3.617A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 558 Processing helix chain 'B' and resid 593 through 603 removed outlier: 4.339A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 649 Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.975A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 95 through 101 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 186 removed outlier: 4.075A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.587A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.754A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 378 through 413 removed outlier: 5.246A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 460 through 465 removed outlier: 4.535A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 4.046A pdb=" N ALA C 480 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 518 removed outlier: 4.019A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.527A pdb=" N LEU C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 514 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.616A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 593 through 603 removed outlier: 4.340A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 649 Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.975A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 186 removed outlier: 4.075A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.587A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.754A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 378 through 413 removed outlier: 5.247A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 460 through 465 removed outlier: 4.535A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 491 removed outlier: 4.047A pdb=" N ALA D 480 " --> pdb=" O PHE D 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 518 removed outlier: 4.020A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.527A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 514 " --> pdb=" O ASN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 528 removed outlier: 3.617A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 558 Processing helix chain 'D' and resid 593 through 603 removed outlier: 4.340A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 649 Processing helix chain 'D' and resid 656 through 673 removed outlier: 3.975A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.728A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 692 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG A 702 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS A 690 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N CYS A 704 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU A 688 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.728A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 692 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.728A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 692 " --> pdb=" O ASP C 700 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG C 702 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS C 690 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N CYS C 704 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 688 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.727A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 692 " --> pdb=" O ASP D 700 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG D 702 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS D 690 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N CYS D 704 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU D 688 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2436 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: 5.52 Time building geometry restraints manager: 7.76 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: 2980 1.31 - 1.44: 5712 1.44 - 1.56: 11320 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20192 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.35: 503 106.35 - 113.27: 10967 113.27 - 120.18: 7151 120.18 - 127.10: 8513 127.10 - 134.01: 262 Bond angle restraints: 27396 Sorted by residual: angle pdb=" C ASN B 259 " pdb=" N SER B 260 " pdb=" CA SER B 260 " ideal model delta sigma weight residual 120.49 129.47 -8.98 1.42e+00 4.96e-01 4.00e+01 angle pdb=" C ASN A 259 " pdb=" N SER A 260 " pdb=" CA SER A 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN D 259 " pdb=" N SER D 260 " pdb=" CA SER D 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN C 259 " pdb=" N SER C 260 " pdb=" CA SER C 260 " ideal model delta sigma weight residual 120.49 129.42 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.82 -16.08 3.00e+00 1.11e-01 2.87e+01 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 10940 18.88 - 37.76: 768 37.76 - 56.65: 108 56.65 - 75.53: 44 75.53 - 94.41: 16 Dihedral angle restraints: 11876 sinusoidal: 4712 harmonic: 7164 Sorted by residual: dihedral pdb=" CA PHE D 161 " pdb=" C PHE D 161 " pdb=" N TYR D 162 " pdb=" CA TYR D 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE C 161 " pdb=" C PHE C 161 " pdb=" N TYR C 162 " pdb=" CA TYR C 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 161 " pdb=" C PHE B 161 " pdb=" N TYR B 162 " pdb=" CA TYR B 162 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2076 0.036 - 0.072: 760 0.072 - 0.107: 221 0.107 - 0.143: 52 0.143 - 0.179: 23 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 3129 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 725 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 726 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 726 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 726 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.044 5.00e-02 4.00e+02 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5459 2.81 - 3.33: 18245 3.33 - 3.86: 32824 3.86 - 4.38: 37229 4.38 - 4.90: 64325 Nonbonded interactions: 158082 Sorted by model distance: nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.292 2.440 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.292 2.440 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.292 2.440 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.293 2.440 nonbonded pdb=" O TRP C 223 " pdb=" OG1 THR C 227 " model vdw 2.304 2.440 ... (remaining 158077 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 16.190 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 52.120 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.004 0.074 20192 Z= 0.218 Angle : 0.804 16.085 27396 Z= 0.390 Chirality : 0.043 0.179 3132 Planarity : 0.006 0.081 3352 Dihedral : 14.011 94.410 7244 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 2412 helix: -0.08 (0.13), residues: 1368 sheet: -0.04 (0.43), residues: 108 loop : -1.79 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS D 169 PHE 0.015 0.001 PHE D 75 TYR 0.034 0.002 TYR D 162 ARG 0.010 0.001 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 481 time to evaluate : 2.238 Fit side-chains REVERT: A 123 LYS cc_start: 0.8090 (tptm) cc_final: 0.7870 (tptm) REVERT: A 189 ASP cc_start: 0.7587 (t0) cc_final: 0.7268 (t0) REVERT: B 123 LYS cc_start: 0.8095 (tptm) cc_final: 0.7876 (tptm) REVERT: B 189 ASP cc_start: 0.7591 (t0) cc_final: 0.7268 (t0) REVERT: C 123 LYS cc_start: 0.8092 (tptm) cc_final: 0.7862 (tptm) REVERT: C 189 ASP cc_start: 0.7582 (t0) cc_final: 0.7267 (t0) REVERT: D 123 LYS cc_start: 0.8085 (tptm) cc_final: 0.7861 (tptm) REVERT: D 189 ASP cc_start: 0.7592 (t0) cc_final: 0.7271 (t0) outliers start: 8 outliers final: 0 residues processed: 489 average time/residue: 1.0933 time to fit residues: 614.0496 Evaluate side-chains 347 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 221 optimal weight: 0.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN D 156 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20192 Z= 0.174 Angle : 0.510 9.504 27396 Z= 0.249 Chirality : 0.037 0.169 3132 Planarity : 0.004 0.059 3352 Dihedral : 6.351 81.288 2784 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.54 % Allowed : 10.73 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2412 helix: 1.16 (0.14), residues: 1376 sheet: 0.74 (0.59), residues: 88 loop : -1.46 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 676 HIS 0.005 0.001 HIS D 521 PHE 0.006 0.001 PHE D 75 TYR 0.024 0.001 TYR A 162 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 358 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.7970 (tptm) cc_final: 0.7761 (tptm) REVERT: A 189 ASP cc_start: 0.7736 (t0) cc_final: 0.7442 (t0) REVERT: A 371 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7112 (mmp-170) REVERT: A 388 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7246 (ttp-170) REVERT: A 433 MET cc_start: 0.7728 (tpt) cc_final: 0.7392 (tpp) REVERT: A 539 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6401 (ptt90) REVERT: A 637 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 640 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8033 (ttp) REVERT: B 123 LYS cc_start: 0.7949 (tptm) cc_final: 0.7741 (tptm) REVERT: B 189 ASP cc_start: 0.7737 (t0) cc_final: 0.7426 (t0) REVERT: B 371 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7107 (mmp-170) REVERT: B 388 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7230 (ttp-170) REVERT: B 538 LEU cc_start: 0.8164 (mm) cc_final: 0.7899 (mm) REVERT: B 539 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6431 (ptt90) REVERT: B 637 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8511 (mt) REVERT: B 640 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: C 189 ASP cc_start: 0.7740 (t0) cc_final: 0.7432 (t0) REVERT: C 371 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7114 (mmp-170) REVERT: C 388 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7243 (ttp-170) REVERT: C 468 MET cc_start: 0.6792 (tmm) cc_final: 0.6509 (tmm) REVERT: C 538 LEU cc_start: 0.8161 (mm) cc_final: 0.7900 (mm) REVERT: C 637 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8510 (mt) REVERT: C 640 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: D 123 LYS cc_start: 0.7957 (tptm) cc_final: 0.7757 (tptm) REVERT: D 189 ASP cc_start: 0.7756 (t0) cc_final: 0.7451 (t0) REVERT: D 371 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7112 (mmp-170) REVERT: D 388 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7237 (ttp-170) REVERT: D 468 MET cc_start: 0.6839 (tmm) cc_final: 0.6554 (tmm) REVERT: D 538 LEU cc_start: 0.8158 (mm) cc_final: 0.7896 (mm) REVERT: D 539 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6444 (ptt90) REVERT: D 637 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8517 (mt) REVERT: D 640 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8038 (ttp) outliers start: 74 outliers final: 48 residues processed: 392 average time/residue: 1.0674 time to fit residues: 482.9857 Evaluate side-chains 383 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 320 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 615 GLN Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.0370 chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 0.0170 chunk 150 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 0.0870 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.0170 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 247 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20192 Z= 0.128 Angle : 0.474 10.235 27396 Z= 0.231 Chirality : 0.035 0.176 3132 Planarity : 0.004 0.048 3352 Dihedral : 5.871 82.388 2784 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.25 % Allowed : 15.47 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2412 helix: 1.55 (0.14), residues: 1404 sheet: 0.71 (0.59), residues: 88 loop : -1.35 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 223 HIS 0.011 0.001 HIS A 269 PHE 0.011 0.001 PHE B 612 TYR 0.013 0.001 TYR A 162 ARG 0.002 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 360 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7740 (t0) cc_final: 0.7430 (t0) REVERT: A 191 HIS cc_start: 0.8223 (m170) cc_final: 0.7981 (m-70) REVERT: A 269 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6322 (t70) REVERT: A 371 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7079 (mmp-170) REVERT: A 388 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7444 (ttp-170) REVERT: A 433 MET cc_start: 0.7683 (tpt) cc_final: 0.7343 (tpp) REVERT: A 473 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: A 520 GLN cc_start: 0.6753 (pm20) cc_final: 0.6429 (pm20) REVERT: A 528 MET cc_start: 0.5531 (mpt) cc_final: 0.5105 (mpp) REVERT: A 539 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6382 (ptt90) REVERT: A 640 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (ttp) REVERT: B 123 LYS cc_start: 0.7896 (tptm) cc_final: 0.7657 (tptm) REVERT: B 189 ASP cc_start: 0.7729 (t0) cc_final: 0.7397 (t0) REVERT: B 371 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7075 (mmp-170) REVERT: B 388 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7194 (ttp-170) REVERT: B 473 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: B 520 GLN cc_start: 0.6761 (pm20) cc_final: 0.6437 (pm20) REVERT: B 528 MET cc_start: 0.5594 (mpt) cc_final: 0.5154 (mpp) REVERT: B 539 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6427 (ptt90) REVERT: B 640 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8010 (ttp) REVERT: C 189 ASP cc_start: 0.7742 (t0) cc_final: 0.7433 (t0) REVERT: C 191 HIS cc_start: 0.8234 (m170) cc_final: 0.7999 (m-70) REVERT: C 269 HIS cc_start: 0.7247 (t70) cc_final: 0.6002 (m90) REVERT: C 371 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7078 (mmp-170) REVERT: C 388 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7461 (ttt180) REVERT: C 433 MET cc_start: 0.7639 (tpt) cc_final: 0.7298 (tpp) REVERT: C 473 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: C 520 GLN cc_start: 0.6749 (pm20) cc_final: 0.6426 (pm20) REVERT: C 528 MET cc_start: 0.5587 (mpt) cc_final: 0.5136 (mpp) REVERT: D 123 LYS cc_start: 0.7890 (tptm) cc_final: 0.7661 (tptm) REVERT: D 189 ASP cc_start: 0.7726 (t0) cc_final: 0.7408 (t0) REVERT: D 269 HIS cc_start: 0.7244 (t70) cc_final: 0.6004 (m90) REVERT: D 371 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7081 (mmp-170) REVERT: D 388 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7460 (ttt180) REVERT: D 473 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: D 520 GLN cc_start: 0.6741 (pm20) cc_final: 0.6425 (pm20) REVERT: D 528 MET cc_start: 0.5591 (mpt) cc_final: 0.5142 (mpp) REVERT: D 539 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6428 (ptt90) REVERT: D 640 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8081 (ttp) outliers start: 47 outliers final: 18 residues processed: 381 average time/residue: 1.1182 time to fit residues: 490.1889 Evaluate side-chains 347 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 314 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 191 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 247 ASN D 191 HIS D 487 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20192 Z= 0.140 Angle : 0.469 8.507 27396 Z= 0.229 Chirality : 0.035 0.189 3132 Planarity : 0.003 0.041 3352 Dihedral : 5.734 79.958 2784 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.92 % Allowed : 17.19 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2412 helix: 1.73 (0.14), residues: 1408 sheet: 0.87 (0.59), residues: 88 loop : -1.26 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 223 HIS 0.005 0.001 HIS A 521 PHE 0.026 0.001 PHE C 161 TYR 0.013 0.001 TYR A 162 ARG 0.005 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 351 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7697 (t0) cc_final: 0.7338 (t0) REVERT: A 191 HIS cc_start: 0.8267 (m170) cc_final: 0.8062 (m-70) REVERT: A 269 HIS cc_start: 0.6643 (m90) cc_final: 0.6112 (t-170) REVERT: A 371 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7162 (mmp-170) REVERT: A 388 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7483 (ttt180) REVERT: A 433 MET cc_start: 0.7689 (tpt) cc_final: 0.7351 (tpp) REVERT: A 520 GLN cc_start: 0.6719 (pm20) cc_final: 0.6414 (pm20) REVERT: A 528 MET cc_start: 0.5679 (mpt) cc_final: 0.5140 (mpp) REVERT: B 189 ASP cc_start: 0.7708 (t0) cc_final: 0.7311 (t0) REVERT: B 191 HIS cc_start: 0.8242 (m170) cc_final: 0.8007 (m-70) REVERT: B 269 HIS cc_start: 0.7362 (t70) cc_final: 0.6196 (m90) REVERT: B 371 ARG cc_start: 0.7864 (mmt90) cc_final: 0.7156 (mmp-170) REVERT: B 388 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7478 (ttt180) REVERT: B 433 MET cc_start: 0.7702 (tpt) cc_final: 0.7358 (tpp) REVERT: B 520 GLN cc_start: 0.6725 (pm20) cc_final: 0.6419 (pm20) REVERT: B 528 MET cc_start: 0.5729 (mpt) cc_final: 0.5117 (mpp) REVERT: B 538 LEU cc_start: 0.8149 (mm) cc_final: 0.7853 (mm) REVERT: B 539 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6368 (ptt90) REVERT: C 189 ASP cc_start: 0.7713 (t0) cc_final: 0.7358 (t0) REVERT: C 269 HIS cc_start: 0.7362 (t70) cc_final: 0.6204 (m90) REVERT: C 371 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7161 (mmp-170) REVERT: C 388 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7484 (ttt180) REVERT: C 433 MET cc_start: 0.7680 (tpt) cc_final: 0.7335 (tpp) REVERT: C 520 GLN cc_start: 0.6716 (pm20) cc_final: 0.6482 (mp10) REVERT: C 528 MET cc_start: 0.5722 (mpt) cc_final: 0.5115 (mpp) REVERT: C 538 LEU cc_start: 0.8147 (mm) cc_final: 0.7852 (mm) REVERT: D 189 ASP cc_start: 0.7678 (t0) cc_final: 0.7284 (t0) REVERT: D 191 HIS cc_start: 0.8242 (m170) cc_final: 0.8001 (m-70) REVERT: D 269 HIS cc_start: 0.7359 (t70) cc_final: 0.6208 (m90) REVERT: D 371 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7162 (mmp-170) REVERT: D 388 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7480 (ttt180) REVERT: D 433 MET cc_start: 0.7688 (tpt) cc_final: 0.7341 (tpp) REVERT: D 520 GLN cc_start: 0.6724 (pm20) cc_final: 0.6419 (pm20) REVERT: D 538 LEU cc_start: 0.8142 (mm) cc_final: 0.7841 (mm) outliers start: 61 outliers final: 40 residues processed: 385 average time/residue: 1.0254 time to fit residues: 458.3942 Evaluate side-chains 362 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 247 ASN A 487 GLN B 247 ASN C 156 GLN C 191 HIS C 247 ASN D 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20192 Z= 0.186 Angle : 0.492 7.964 27396 Z= 0.242 Chirality : 0.037 0.195 3132 Planarity : 0.003 0.038 3352 Dihedral : 5.925 75.494 2784 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.83 % Allowed : 16.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2412 helix: 1.75 (0.14), residues: 1408 sheet: 0.84 (0.58), residues: 88 loop : -1.23 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 223 HIS 0.005 0.001 HIS D 165 PHE 0.017 0.001 PHE D 161 TYR 0.014 0.001 TYR D 162 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 356 time to evaluate : 2.178 Fit side-chains REVERT: A 189 ASP cc_start: 0.7680 (t0) cc_final: 0.7256 (t0) REVERT: A 191 HIS cc_start: 0.8274 (m170) cc_final: 0.8055 (m-70) REVERT: A 269 HIS cc_start: 0.6797 (m90) cc_final: 0.6479 (t-170) REVERT: A 371 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7219 (mmp-170) REVERT: A 388 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7505 (ttt180) REVERT: A 406 ILE cc_start: 0.8836 (mm) cc_final: 0.8558 (mt) REVERT: A 433 MET cc_start: 0.7699 (tpt) cc_final: 0.7372 (tpp) REVERT: A 539 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6457 (ptt90) REVERT: B 189 ASP cc_start: 0.7675 (t0) cc_final: 0.7211 (t0) REVERT: B 191 HIS cc_start: 0.8283 (m170) cc_final: 0.8033 (m-70) REVERT: B 269 HIS cc_start: 0.7432 (t70) cc_final: 0.6443 (m90) REVERT: B 371 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7209 (mmp-170) REVERT: B 388 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7510 (ttt180) REVERT: B 406 ILE cc_start: 0.8844 (mm) cc_final: 0.8585 (mt) REVERT: B 433 MET cc_start: 0.7715 (tpt) cc_final: 0.7381 (tpp) REVERT: B 538 LEU cc_start: 0.8151 (mm) cc_final: 0.7811 (mm) REVERT: B 539 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6373 (ppt90) REVERT: C 123 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7245 (tptm) REVERT: C 189 ASP cc_start: 0.7658 (t0) cc_final: 0.7213 (t0) REVERT: C 191 HIS cc_start: 0.8255 (m170) cc_final: 0.7983 (m-70) REVERT: C 269 HIS cc_start: 0.7430 (t70) cc_final: 0.6443 (m90) REVERT: C 371 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7217 (mmp-170) REVERT: C 388 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7508 (ttt180) REVERT: C 406 ILE cc_start: 0.8846 (mm) cc_final: 0.8581 (mt) REVERT: C 538 LEU cc_start: 0.8146 (mm) cc_final: 0.7813 (mm) REVERT: C 539 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6513 (ptt90) REVERT: D 189 ASP cc_start: 0.7662 (t0) cc_final: 0.7201 (t0) REVERT: D 191 HIS cc_start: 0.8283 (m170) cc_final: 0.8024 (m-70) REVERT: D 269 HIS cc_start: 0.7441 (t70) cc_final: 0.6441 (m90) REVERT: D 371 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7214 (mmp-170) REVERT: D 388 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7496 (ttt180) REVERT: D 406 ILE cc_start: 0.8850 (mm) cc_final: 0.8583 (mt) REVERT: D 433 MET cc_start: 0.7670 (tpt) cc_final: 0.7339 (tpp) REVERT: D 538 LEU cc_start: 0.8142 (mm) cc_final: 0.7801 (mm) REVERT: D 539 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6537 (ptt90) outliers start: 80 outliers final: 44 residues processed: 409 average time/residue: 1.0037 time to fit residues: 477.3703 Evaluate side-chains 384 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN D 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20192 Z= 0.185 Angle : 0.489 7.959 27396 Z= 0.239 Chirality : 0.037 0.209 3132 Planarity : 0.003 0.037 3352 Dihedral : 5.940 73.578 2784 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.89 % Allowed : 16.43 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2412 helix: 1.77 (0.14), residues: 1412 sheet: 0.72 (0.57), residues: 88 loop : -1.12 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 223 HIS 0.004 0.001 HIS B 521 PHE 0.017 0.001 PHE B 161 TYR 0.008 0.001 TYR B 403 ARG 0.004 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 336 time to evaluate : 2.053 Fit side-chains REVERT: A 189 ASP cc_start: 0.7636 (t0) cc_final: 0.7188 (t0) REVERT: A 191 HIS cc_start: 0.8296 (m170) cc_final: 0.8076 (m-70) REVERT: A 269 HIS cc_start: 0.6824 (m90) cc_final: 0.6467 (t-170) REVERT: A 371 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7211 (mmp-170) REVERT: A 388 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (ttt180) REVERT: A 406 ILE cc_start: 0.8853 (mm) cc_final: 0.8585 (mt) REVERT: A 528 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.5166 (mpt) REVERT: B 173 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7181 (t0) REVERT: B 191 HIS cc_start: 0.8295 (m170) cc_final: 0.8044 (m-70) REVERT: B 371 ARG cc_start: 0.7874 (mmt90) cc_final: 0.7220 (mmp-170) REVERT: B 388 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7484 (ttt180) REVERT: B 406 ILE cc_start: 0.8859 (mm) cc_final: 0.8624 (mt) REVERT: B 433 MET cc_start: 0.7700 (tpt) cc_final: 0.7377 (tpp) REVERT: B 528 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5074 (mpp) REVERT: C 123 LYS cc_start: 0.7883 (tttt) cc_final: 0.7443 (tppp) REVERT: C 173 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 189 ASP cc_start: 0.7612 (t0) cc_final: 0.7138 (t0) REVERT: C 191 HIS cc_start: 0.8298 (m170) cc_final: 0.8017 (m-70) REVERT: C 269 HIS cc_start: 0.7481 (t70) cc_final: 0.6613 (m170) REVERT: C 371 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7210 (mmp-170) REVERT: C 388 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7495 (ttt180) REVERT: C 406 ILE cc_start: 0.8854 (mm) cc_final: 0.8604 (mt) REVERT: C 528 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.5091 (mpp) REVERT: D 173 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 189 ASP cc_start: 0.7650 (t0) cc_final: 0.7167 (t0) REVERT: D 191 HIS cc_start: 0.8281 (m170) cc_final: 0.8022 (m-70) REVERT: D 269 HIS cc_start: 0.7489 (t70) cc_final: 0.6612 (m170) REVERT: D 371 ARG cc_start: 0.7870 (mmt90) cc_final: 0.7208 (mmp-170) REVERT: D 388 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7476 (ttt180) REVERT: D 406 ILE cc_start: 0.8842 (mm) cc_final: 0.8597 (mt) REVERT: D 528 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5056 (mpp) outliers start: 102 outliers final: 57 residues processed: 402 average time/residue: 1.0108 time to fit residues: 471.8697 Evaluate side-chains 394 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.4980 chunk 26 optimal weight: 0.0010 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 0.0270 chunk 133 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 414 GLN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20192 Z= 0.134 Angle : 0.476 8.126 27396 Z= 0.231 Chirality : 0.036 0.216 3132 Planarity : 0.003 0.034 3352 Dihedral : 5.697 75.073 2784 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.30 % Allowed : 18.34 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2412 helix: 1.94 (0.14), residues: 1408 sheet: 0.71 (0.57), residues: 88 loop : -1.08 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.004 0.001 HIS D 521 PHE 0.015 0.001 PHE C 161 TYR 0.007 0.001 TYR C 162 ARG 0.005 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 352 time to evaluate : 2.211 Fit side-chains REVERT: A 189 ASP cc_start: 0.7615 (t0) cc_final: 0.7157 (t0) REVERT: A 191 HIS cc_start: 0.8306 (m170) cc_final: 0.8064 (m-70) REVERT: A 269 HIS cc_start: 0.6855 (m90) cc_final: 0.6500 (t70) REVERT: A 371 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7222 (mmp-170) REVERT: A 388 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: A 406 ILE cc_start: 0.8835 (mm) cc_final: 0.8548 (mt) REVERT: A 528 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5091 (mpp) REVERT: A 538 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 173 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 189 ASP cc_start: 0.7646 (t0) cc_final: 0.7126 (t0) REVERT: B 191 HIS cc_start: 0.8289 (m170) cc_final: 0.8000 (m-70) REVERT: B 327 SER cc_start: 0.8904 (m) cc_final: 0.8702 (t) REVERT: B 371 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7232 (mmp-170) REVERT: B 388 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7265 (mtm-85) REVERT: B 406 ILE cc_start: 0.8835 (mm) cc_final: 0.8566 (mt) REVERT: B 433 MET cc_start: 0.7688 (tpt) cc_final: 0.7366 (tpp) REVERT: B 528 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5114 (mpp) REVERT: C 173 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 189 ASP cc_start: 0.7613 (t0) cc_final: 0.7142 (t0) REVERT: C 191 HIS cc_start: 0.8281 (m170) cc_final: 0.7968 (m-70) REVERT: C 269 HIS cc_start: 0.7463 (t70) cc_final: 0.6608 (m170) REVERT: C 371 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7235 (mmp-170) REVERT: C 388 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7413 (mtp180) REVERT: C 406 ILE cc_start: 0.8840 (mm) cc_final: 0.8573 (mt) REVERT: C 528 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5063 (mpp) REVERT: D 189 ASP cc_start: 0.7621 (t0) cc_final: 0.7113 (t0) REVERT: D 191 HIS cc_start: 0.8281 (m170) cc_final: 0.7985 (m-70) REVERT: D 269 HIS cc_start: 0.7470 (t70) cc_final: 0.6603 (m170) REVERT: D 371 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7218 (mmp-170) REVERT: D 388 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7276 (mtm-85) REVERT: D 528 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5091 (mpp) outliers start: 69 outliers final: 40 residues processed: 390 average time/residue: 0.9833 time to fit residues: 454.7295 Evaluate side-chains 389 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 340 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 184 optimal weight: 0.0370 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 413 HIS B 247 ASN B 413 HIS C 247 ASN C 413 HIS C 655 ASN D 247 ASN D 414 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20192 Z= 0.135 Angle : 0.485 9.126 27396 Z= 0.234 Chirality : 0.036 0.232 3132 Planarity : 0.003 0.032 3352 Dihedral : 5.615 75.386 2784 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.92 % Allowed : 19.25 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2412 helix: 2.02 (0.14), residues: 1408 sheet: 0.75 (0.56), residues: 88 loop : -0.98 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 223 HIS 0.003 0.001 HIS D 521 PHE 0.014 0.001 PHE C 161 TYR 0.008 0.001 TYR C 162 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 357 time to evaluate : 2.211 Fit side-chains REVERT: A 189 ASP cc_start: 0.7620 (t0) cc_final: 0.7145 (t0) REVERT: A 191 HIS cc_start: 0.8287 (m170) cc_final: 0.8040 (m-70) REVERT: A 269 HIS cc_start: 0.6793 (m90) cc_final: 0.6472 (t70) REVERT: A 371 ARG cc_start: 0.7874 (mmt90) cc_final: 0.7224 (mmp-170) REVERT: A 388 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7295 (mtm-85) REVERT: A 406 ILE cc_start: 0.8819 (mm) cc_final: 0.8518 (mt) REVERT: A 528 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5107 (mpp) REVERT: A 645 MET cc_start: 0.6761 (tpp) cc_final: 0.6550 (ttm) REVERT: B 173 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7653 (tm-30) REVERT: B 189 ASP cc_start: 0.7634 (t0) cc_final: 0.7124 (t0) REVERT: B 191 HIS cc_start: 0.8290 (m170) cc_final: 0.8005 (m-70) REVERT: B 371 ARG cc_start: 0.7864 (mmt90) cc_final: 0.7220 (mmp-170) REVERT: B 388 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7409 (mtp180) REVERT: B 406 ILE cc_start: 0.8866 (mm) cc_final: 0.8572 (mt) REVERT: B 433 MET cc_start: 0.7688 (tpt) cc_final: 0.7336 (tpp) REVERT: B 528 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5132 (mpp) REVERT: C 173 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 189 ASP cc_start: 0.7615 (t0) cc_final: 0.7112 (t0) REVERT: C 269 HIS cc_start: 0.7478 (t70) cc_final: 0.6605 (m170) REVERT: C 371 ARG cc_start: 0.7868 (mmt90) cc_final: 0.7217 (mmp-170) REVERT: C 388 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: C 406 ILE cc_start: 0.8836 (mm) cc_final: 0.8543 (mt) REVERT: C 528 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5078 (mpp) REVERT: C 645 MET cc_start: 0.6766 (tpp) cc_final: 0.6452 (ttp) REVERT: D 189 ASP cc_start: 0.7625 (t0) cc_final: 0.7110 (t0) REVERT: D 191 HIS cc_start: 0.8265 (m170) cc_final: 0.7959 (m-70) REVERT: D 269 HIS cc_start: 0.7492 (t70) cc_final: 0.6610 (m170) REVERT: D 371 ARG cc_start: 0.7868 (mmt90) cc_final: 0.7221 (mmp-170) REVERT: D 388 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7412 (mtp180) REVERT: D 528 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5108 (mpp) outliers start: 61 outliers final: 40 residues processed: 384 average time/residue: 0.9849 time to fit residues: 442.7895 Evaluate side-chains 387 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 339 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN C 247 ASN D 247 ASN D 413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20192 Z= 0.178 Angle : 0.517 10.068 27396 Z= 0.248 Chirality : 0.037 0.237 3132 Planarity : 0.003 0.033 3352 Dihedral : 5.778 73.180 2784 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.16 % Allowed : 19.16 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2412 helix: 1.93 (0.14), residues: 1416 sheet: 0.83 (0.56), residues: 88 loop : -1.04 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 223 HIS 0.003 0.001 HIS A 251 PHE 0.015 0.001 PHE C 161 TYR 0.009 0.001 TYR B 403 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 346 time to evaluate : 2.378 Fit side-chains REVERT: A 173 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 189 ASP cc_start: 0.7636 (t0) cc_final: 0.7135 (t0) REVERT: A 191 HIS cc_start: 0.8308 (m170) cc_final: 0.8065 (m-70) REVERT: A 269 HIS cc_start: 0.6864 (m90) cc_final: 0.6584 (t70) REVERT: A 371 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7168 (mmp-170) REVERT: A 388 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7249 (mtm-85) REVERT: A 406 ILE cc_start: 0.8833 (mm) cc_final: 0.8531 (mt) REVERT: A 528 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5101 (mpp) REVERT: A 538 LEU cc_start: 0.8270 (mm) cc_final: 0.7966 (mp) REVERT: B 173 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 189 ASP cc_start: 0.7639 (t0) cc_final: 0.7139 (t0) REVERT: B 191 HIS cc_start: 0.8293 (m170) cc_final: 0.8031 (m-70) REVERT: B 371 ARG cc_start: 0.7889 (mmt90) cc_final: 0.7171 (mmp-170) REVERT: B 388 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7276 (mtm-85) REVERT: B 406 ILE cc_start: 0.8838 (mm) cc_final: 0.8547 (mt) REVERT: B 433 MET cc_start: 0.7690 (tpt) cc_final: 0.7338 (tpp) REVERT: B 528 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.5111 (mpp) REVERT: B 645 MET cc_start: 0.6634 (ttm) cc_final: 0.5533 (ttp) REVERT: C 173 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 189 ASP cc_start: 0.7601 (t0) cc_final: 0.7100 (t0) REVERT: C 191 HIS cc_start: 0.8282 (m170) cc_final: 0.7976 (m-70) REVERT: C 269 HIS cc_start: 0.7487 (t70) cc_final: 0.6625 (m170) REVERT: C 371 ARG cc_start: 0.7894 (mmt90) cc_final: 0.7168 (mmp-170) REVERT: C 388 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: C 406 ILE cc_start: 0.8852 (mm) cc_final: 0.8574 (mt) REVERT: C 528 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5072 (mpp) REVERT: D 173 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 189 ASP cc_start: 0.7631 (t0) cc_final: 0.7117 (t0) REVERT: D 191 HIS cc_start: 0.8277 (m170) cc_final: 0.7984 (m-70) REVERT: D 269 HIS cc_start: 0.7502 (t70) cc_final: 0.6633 (m170) REVERT: D 371 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7168 (mmp-170) REVERT: D 388 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7400 (mtp180) REVERT: D 528 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.5103 (mpp) outliers start: 66 outliers final: 44 residues processed: 382 average time/residue: 0.9855 time to fit residues: 439.4281 Evaluate side-chains 395 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 343 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 243 optimal weight: 0.0980 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20192 Z= 0.177 Angle : 0.528 11.627 27396 Z= 0.252 Chirality : 0.037 0.241 3132 Planarity : 0.003 0.034 3352 Dihedral : 5.813 72.433 2784 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 20.02 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2412 helix: 1.93 (0.14), residues: 1416 sheet: 0.86 (0.56), residues: 88 loop : -1.02 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 223 HIS 0.003 0.001 HIS D 251 PHE 0.014 0.001 PHE C 161 TYR 0.009 0.001 TYR B 403 ARG 0.004 0.000 ARG C 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 353 time to evaluate : 2.412 Fit side-chains REVERT: A 173 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 189 ASP cc_start: 0.7627 (t0) cc_final: 0.7118 (t0) REVERT: A 191 HIS cc_start: 0.8288 (m170) cc_final: 0.8038 (m-70) REVERT: A 269 HIS cc_start: 0.6850 (m90) cc_final: 0.6594 (t70) REVERT: A 371 ARG cc_start: 0.7894 (mmt90) cc_final: 0.7166 (mmp-170) REVERT: A 388 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7261 (mtm-85) REVERT: A 406 ILE cc_start: 0.8814 (mm) cc_final: 0.8500 (mt) REVERT: A 528 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5086 (mpp) REVERT: A 538 LEU cc_start: 0.8275 (mm) cc_final: 0.7971 (mp) REVERT: B 173 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 189 ASP cc_start: 0.7620 (t0) cc_final: 0.7089 (t0) REVERT: B 191 HIS cc_start: 0.8286 (m170) cc_final: 0.7992 (m-70) REVERT: B 371 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7166 (mmp-170) REVERT: B 388 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7260 (mtm-85) REVERT: B 406 ILE cc_start: 0.8814 (mm) cc_final: 0.8515 (mt) REVERT: B 528 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5104 (mpp) REVERT: C 173 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 189 ASP cc_start: 0.7614 (t0) cc_final: 0.7113 (t0) REVERT: C 191 HIS cc_start: 0.8285 (m170) cc_final: 0.7968 (m-70) REVERT: C 371 ARG cc_start: 0.7894 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: C 388 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7266 (mtm-85) REVERT: C 406 ILE cc_start: 0.8817 (mm) cc_final: 0.8526 (mt) REVERT: C 528 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5074 (mpp) REVERT: D 173 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 189 ASP cc_start: 0.7611 (t0) cc_final: 0.7099 (t0) REVERT: D 191 HIS cc_start: 0.8272 (m170) cc_final: 0.7958 (m-70) REVERT: D 371 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: D 388 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: D 528 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5096 (mpp) outliers start: 56 outliers final: 43 residues processed: 379 average time/residue: 0.9755 time to fit residues: 432.2929 Evaluate side-chains 398 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 347 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN C 655 ASN D 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.152528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121688 restraints weight = 23270.361| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.72 r_work: 0.3218 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20192 Z= 0.178 Angle : 0.529 12.484 27396 Z= 0.253 Chirality : 0.037 0.241 3132 Planarity : 0.003 0.034 3352 Dihedral : 5.831 71.804 2784 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.97 % Allowed : 19.68 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2412 helix: 1.95 (0.14), residues: 1416 sheet: 0.76 (0.56), residues: 88 loop : -1.00 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 223 HIS 0.003 0.001 HIS A 251 PHE 0.014 0.001 PHE C 161 TYR 0.009 0.001 TYR A 403 ARG 0.004 0.000 ARG C 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7592.58 seconds wall clock time: 135 minutes 50.20 seconds (8150.20 seconds total)