Starting phenix.real_space_refine on Sun Mar 24 18:00:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlu_11274/03_2024/6zlu_11274.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21700 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 13742 2.51 5 N 3652 2.21 5 O 4226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B GLU 721": "OE1" <-> "OE2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ASP 873": "OD1" <-> "OD2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 996": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D GLU 721": "OE1" <-> "OE2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 774": "OE1" <-> "OE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D GLU 868": "OE1" <-> "OE2" Residue "D ASP 873": "OD1" <-> "OD2" Residue "D GLU 944": "OE1" <-> "OE2" Residue "D GLU 996": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21700 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4457 Classifications: {'peptide': 555} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 535} Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6393 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 776} Chain: "C" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4457 Classifications: {'peptide': 555} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 535} Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6393 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 776} Time building chain proxies: 11.13, per 1000 atoms: 0.51 Number of scatterers: 21700 At special positions: 0 Unit cell: (157.29, 92.02, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 4226 8.00 N 3652 7.00 C 13742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.11 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.11 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: 7.85 Conformation dependent library (CDL) restraints added in 3.8 seconds 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 26 sheets defined 28.8% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.994A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 24 through 39 removed outlier: 4.558A pdb=" N TRP A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.573A pdb=" N VAL A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.939A pdb=" N GLN A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 142 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 166 through 185 removed outlier: 3.651A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 4.046A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.656A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.549A pdb=" N LEU A 258 " --> pdb=" O MET A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.598A pdb=" N GLU A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.735A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 500 through 514 removed outlier: 4.516A pdb=" N SER A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.888A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 3.785A pdb=" N ASN A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.523A pdb=" N ASN B 255 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 602 through 608 removed outlier: 5.110A pdb=" N ASN B 605 " --> pdb=" O THR B 602 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE B 606 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 779 through 786 removed outlier: 3.522A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 821 removed outlier: 3.714A pdb=" N VAL B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 895 removed outlier: 3.863A pdb=" N LYS B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.869A pdb=" N LEU B 911 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 967 through 969 No H-bonds generated for 'chain 'B' and resid 967 through 969' Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.994A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Proline residue: C 22 - end of helix Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.558A pdb=" N TRP C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.573A pdb=" N VAL C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 84 through 110 removed outlier: 3.939A pdb=" N GLN C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 142 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.651A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 4.046A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.656A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.549A pdb=" N LEU C 258 " --> pdb=" O MET C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.598A pdb=" N GLU C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.735A pdb=" N PHE C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 407 through 421 Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 500 through 514 removed outlier: 4.516A pdb=" N SER C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.888A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.785A pdb=" N ASN C 543 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.523A pdb=" N ASN D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 376 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 584 through 587 Processing helix chain 'D' and resid 602 through 608 removed outlier: 5.110A pdb=" N ASN D 605 " --> pdb=" O THR D 602 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE D 606 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 779 through 786 removed outlier: 3.522A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.714A pdb=" N VAL D 819 " --> pdb=" O SER D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 895 removed outlier: 3.863A pdb=" N LYS D 893 " --> pdb=" O ASP D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 914 removed outlier: 3.869A pdb=" N LEU D 911 " --> pdb=" O GLY D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 941 No H-bonds generated for 'chain 'D' and resid 939 through 941' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 967 through 969 No H-bonds generated for 'chain 'D' and resid 967 through 969' Processing sheet with id= 1, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.024A pdb=" N GLY A 61 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 301 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.924A pdb=" N SER A 267 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG A 406 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP A 269 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 313 through 314 removed outlier: 4.053A pdb=" N ASN A 336 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 345 through 346 Processing sheet with id= 5, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= 6, first strand: chain 'B' and resid 214 through 224 removed outlier: 4.368A pdb=" N ARG B 421 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG B 457 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 740 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 873 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 956 " --> pdb=" O ASP B 873 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 875 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 954 " --> pdb=" O THR B 875 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 877 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 983 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN B 953 " --> pdb=" O ASN B 981 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 981 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 955 " --> pdb=" O ALA B 979 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B 979 " --> pdb=" O GLN B 955 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY B 957 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS B 977 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR B 959 " --> pdb=" O PHE B 975 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE B 975 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 972 " --> pdb=" O GLY B1015 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.772A pdb=" N ALA B 260 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET B 276 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B 262 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 464 through 465 Processing sheet with id= 9, first strand: chain 'B' and resid 638 through 640 removed outlier: 6.377A pdb=" N ILE B 638 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= 11, first strand: chain 'B' and resid 804 through 807 removed outlier: 6.580A pdb=" N GLN B 804 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.870A pdb=" N ARG B 834 " --> pdb=" O ASP B 810 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 885 through 887 Processing sheet with id= 14, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.024A pdb=" N GLY C 61 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 301 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.924A pdb=" N SER C 267 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG C 406 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP C 269 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.053A pdb=" N ASN C 336 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 345 through 346 Processing sheet with id= 18, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= 19, first strand: chain 'D' and resid 214 through 224 removed outlier: 4.368A pdb=" N ARG D 421 " --> pdb=" O ARG D 457 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 457 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA D 740 " --> pdb=" O LEU D 776 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP D 873 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 956 " --> pdb=" O ASP D 873 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 875 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE D 954 " --> pdb=" O THR D 875 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE D 877 " --> pdb=" O ARG D 952 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 983 " --> pdb=" O LEU D 951 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN D 953 " --> pdb=" O ASN D 981 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN D 981 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN D 955 " --> pdb=" O ALA D 979 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA D 979 " --> pdb=" O GLN D 955 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY D 957 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS D 977 " --> pdb=" O GLY D 957 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR D 959 " --> pdb=" O PHE D 975 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE D 975 " --> pdb=" O THR D 959 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 972 " --> pdb=" O GLY D1015 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.772A pdb=" N ALA D 260 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET D 276 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN D 262 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 464 through 465 Processing sheet with id= 22, first strand: chain 'D' and resid 638 through 640 removed outlier: 6.377A pdb=" N ILE D 638 " --> pdb=" O ASN D 676 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 719 through 722 Processing sheet with id= 24, first strand: chain 'D' and resid 804 through 807 removed outlier: 6.580A pdb=" N GLN D 804 " --> pdb=" O ILE D 852 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 809 through 812 removed outlier: 4.870A pdb=" N ARG D 834 " --> pdb=" O ASP D 810 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 885 through 887 1060 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7044 1.34 - 1.47: 6006 1.47 - 1.60: 9050 1.60 - 1.73: 0 1.73 - 1.86: 142 Bond restraints: 22242 Sorted by residual: bond pdb=" CB ASN D 470 " pdb=" CG ASN D 470 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB ASN B 470 " pdb=" CG ASN B 470 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB ASN B 785 " pdb=" CG ASN B 785 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" CB ASN D 785 " pdb=" CG ASN D 785 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" C THR B 469 " pdb=" N ASN B 470 " ideal model delta sigma weight residual 1.336 1.306 0.030 1.55e-02 4.16e+03 3.85e+00 ... (remaining 22237 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.68: 366 105.68 - 112.79: 10600 112.79 - 119.89: 8326 119.89 - 127.00: 10614 127.00 - 134.10: 264 Bond angle restraints: 30170 Sorted by residual: angle pdb=" CA TRP D 599 " pdb=" CB TRP D 599 " pdb=" CG TRP D 599 " ideal model delta sigma weight residual 113.60 122.41 -8.81 1.90e+00 2.77e-01 2.15e+01 angle pdb=" CA TRP B 599 " pdb=" CB TRP B 599 " pdb=" CG TRP B 599 " ideal model delta sigma weight residual 113.60 122.41 -8.81 1.90e+00 2.77e-01 2.15e+01 angle pdb=" CG ARG B 588 " pdb=" CD ARG B 588 " pdb=" NE ARG B 588 " ideal model delta sigma weight residual 112.00 103.31 8.69 2.20e+00 2.07e-01 1.56e+01 angle pdb=" CG ARG D 588 " pdb=" CD ARG D 588 " pdb=" NE ARG D 588 " ideal model delta sigma weight residual 112.00 103.31 8.69 2.20e+00 2.07e-01 1.56e+01 angle pdb=" C PRO B 405 " pdb=" N ASP B 406 " pdb=" CA ASP B 406 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 ... (remaining 30165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11306 17.80 - 35.60: 1268 35.60 - 53.39: 292 53.39 - 71.19: 76 71.19 - 88.99: 42 Dihedral angle restraints: 12984 sinusoidal: 5132 harmonic: 7852 Sorted by residual: dihedral pdb=" CA ASN B 470 " pdb=" C ASN B 470 " pdb=" N ASN B 471 " pdb=" CA ASN B 471 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN D 470 " pdb=" C ASN D 470 " pdb=" N ASN D 471 " pdb=" CA ASN D 471 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR D 645 " pdb=" C THR D 645 " pdb=" N THR D 646 " pdb=" CA THR D 646 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2662 0.078 - 0.157: 434 0.157 - 0.235: 10 0.235 - 0.314: 4 0.314 - 0.392: 2 Chirality restraints: 3112 Sorted by residual: chirality pdb=" CB ILE B 377 " pdb=" CA ILE B 377 " pdb=" CG1 ILE B 377 " pdb=" CG2 ILE B 377 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE C 275 " pdb=" CA ILE C 275 " pdb=" CG1 ILE C 275 " pdb=" CG2 ILE C 275 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3109 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 384 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO B 385 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 384 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO D 385 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 385 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 385 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 303 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO C 304 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 304 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 304 " -0.040 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 26 2.11 - 2.81: 6400 2.81 - 3.51: 29591 3.51 - 4.20: 56690 4.20 - 4.90: 95950 Nonbonded interactions: 188657 Sorted by model distance: nonbonded pdb=" O CYS A 1 " pdb=" OH TYR B 589 " model vdw 1.417 2.440 nonbonded pdb=" O CYS C 1 " pdb=" OH TYR D 589 " model vdw 1.417 2.440 nonbonded pdb=" OG1 THR C 82 " pdb=" OE2 GLU D 846 " model vdw 1.616 2.440 nonbonded pdb=" OG1 THR A 82 " pdb=" OE2 GLU B 846 " model vdw 1.616 2.440 nonbonded pdb=" O GLY B 547 " pdb=" OD2 ASP D 537 " model vdw 1.667 3.040 ... (remaining 188652 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 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 5.170 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 56.620 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 22242 Z= 0.512 Angle : 0.993 8.978 30170 Z= 0.558 Chirality : 0.055 0.392 3112 Planarity : 0.006 0.074 3968 Dihedral : 16.839 88.989 8016 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.65 % Favored : 94.91 % Rotamer: Outliers : 0.09 % Allowed : 19.70 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 2710 helix: -2.71 (0.15), residues: 612 sheet: -0.23 (0.18), residues: 722 loop : -1.27 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP D 425 HIS 0.009 0.002 HIS D 362 PHE 0.026 0.004 PHE D 942 TYR 0.021 0.004 TYR D 712 ARG 0.008 0.001 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 582 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TRP cc_start: 0.4518 (m-10) cc_final: 0.3827 (m100) REVERT: B 273 LEU cc_start: 0.5763 (tp) cc_final: 0.5486 (pt) REVERT: B 422 TYR cc_start: 0.6631 (p90) cc_final: 0.6219 (p90) REVERT: B 511 LEU cc_start: 0.7838 (mt) cc_final: 0.7605 (mt) REVERT: B 841 ASN cc_start: 0.6442 (p0) cc_final: 0.6134 (m-40) REVERT: C 290 LEU cc_start: 0.5441 (mt) cc_final: 0.4958 (mt) REVERT: C 295 ILE cc_start: 0.2150 (tp) cc_final: 0.1866 (tp) REVERT: C 385 PRO cc_start: 0.5074 (Cg_exo) cc_final: 0.4788 (Cg_endo) REVERT: D 273 LEU cc_start: 0.6499 (tp) cc_final: 0.6044 (pt) REVERT: D 309 ASN cc_start: 0.8356 (t0) cc_final: 0.8147 (t0) REVERT: D 450 ASP cc_start: 0.6597 (t0) cc_final: 0.5784 (m-30) REVERT: D 770 THR cc_start: 0.2426 (t) cc_final: 0.1825 (m) REVERT: D 841 ASN cc_start: 0.6971 (p0) cc_final: 0.6499 (m-40) outliers start: 2 outliers final: 0 residues processed: 584 average time/residue: 0.3468 time to fit residues: 304.3921 Evaluate side-chains 340 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 43 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 263 ASN A 272 GLN A 302 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 538 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 680 ASN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 512 ASN D 676 ASN ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 ASN ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22242 Z= 0.254 Angle : 0.679 10.618 30170 Z= 0.370 Chirality : 0.047 0.274 3112 Planarity : 0.005 0.059 3968 Dihedral : 5.627 23.796 3014 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.36 % Favored : 97.49 % Rotamer: Outliers : 0.17 % Allowed : 2.53 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.60 (0.15), residues: 2710 helix: -0.62 (0.19), residues: 620 sheet: 0.14 (0.17), residues: 766 loop : -0.49 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 599 HIS 0.006 0.001 HIS A 343 PHE 0.045 0.002 PHE A 178 TYR 0.039 0.002 TYR C 203 ARG 0.011 0.001 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 445 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 LEU cc_start: 0.6717 (mt) cc_final: 0.6255 (mp) REVERT: A 498 TRP cc_start: 0.4914 (m-10) cc_final: 0.4105 (m100) REVERT: A 548 GLN cc_start: 0.7528 (tp-100) cc_final: 0.7230 (mt0) REVERT: B 229 MET cc_start: 0.6990 (tpt) cc_final: 0.6767 (tpp) REVERT: B 273 LEU cc_start: 0.6767 (tp) cc_final: 0.6067 (pt) REVERT: B 463 TYR cc_start: 0.5753 (p90) cc_final: 0.5195 (p90) REVERT: B 542 THR cc_start: 0.8800 (m) cc_final: 0.8133 (p) REVERT: B 643 TYR cc_start: 0.7970 (t80) cc_final: 0.7498 (t80) REVERT: B 770 THR cc_start: 0.1660 (t) cc_final: 0.1266 (m) REVERT: B 970 MET cc_start: 0.4118 (mtp) cc_final: 0.3841 (mtm) REVERT: C 168 ASP cc_start: 0.7382 (p0) cc_final: 0.6908 (p0) REVERT: C 290 LEU cc_start: 0.6139 (mt) cc_final: 0.5667 (mt) REVERT: C 352 TYR cc_start: 0.3465 (t80) cc_final: 0.3000 (t80) REVERT: C 360 ILE cc_start: 0.5992 (mm) cc_final: 0.5770 (mt) REVERT: D 273 LEU cc_start: 0.6806 (tp) cc_final: 0.6399 (pt) REVERT: D 388 ILE cc_start: 0.7911 (mm) cc_final: 0.7592 (mm) REVERT: D 427 MET cc_start: 0.6649 (mpp) cc_final: 0.6361 (mpp) REVERT: D 533 TYR cc_start: 0.3105 (t80) cc_final: 0.2064 (t80) outliers start: 4 outliers final: 1 residues processed: 449 average time/residue: 0.3530 time to fit residues: 238.6383 Evaluate side-chains 294 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 218 optimal weight: 0.0170 chunk 243 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 overall best weight: 2.6034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 139 GLN A 306 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 417 ASN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN B 480 GLN B 737 ASN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 999 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS C 327 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 ASN D 999 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22242 Z= 0.345 Angle : 0.783 14.119 30170 Z= 0.416 Chirality : 0.050 0.265 3112 Planarity : 0.005 0.083 3968 Dihedral : 5.813 22.421 3014 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 0.31 % Allowed : 4.18 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.45 (0.15), residues: 2710 helix: -0.49 (0.19), residues: 662 sheet: 0.39 (0.17), residues: 752 loop : -0.50 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 479 HIS 0.010 0.003 HIS D 799 PHE 0.043 0.002 PHE C 178 TYR 0.027 0.002 TYR D 458 ARG 0.011 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 383 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6112 (p90) cc_final: 0.5706 (p90) REVERT: A 476 MET cc_start: 0.5981 (mmp) cc_final: 0.5575 (mmp) REVERT: A 548 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7749 (mt0) REVERT: B 229 MET cc_start: 0.7479 (tpt) cc_final: 0.7240 (tpp) REVERT: B 330 ASN cc_start: 0.7736 (t0) cc_final: 0.7335 (t0) REVERT: B 339 PHE cc_start: 0.7095 (t80) cc_final: 0.6832 (t80) REVERT: B 524 GLU cc_start: 0.6680 (pt0) cc_final: 0.6264 (pt0) REVERT: B 529 LEU cc_start: 0.7589 (mt) cc_final: 0.7374 (mp) REVERT: B 643 TYR cc_start: 0.8101 (t80) cc_final: 0.7440 (t80) REVERT: B 970 MET cc_start: 0.4803 (mtp) cc_final: 0.4583 (ttp) REVERT: C 152 MET cc_start: 0.7463 (ptm) cc_final: 0.6861 (ptm) REVERT: C 168 ASP cc_start: 0.7303 (p0) cc_final: 0.6779 (p0) REVERT: C 242 MET cc_start: 0.5734 (mmt) cc_final: 0.5110 (mmt) REVERT: D 273 LEU cc_start: 0.7343 (tp) cc_final: 0.6725 (pt) REVERT: D 481 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7773 (tt0) REVERT: D 897 TRP cc_start: 0.6956 (t-100) cc_final: 0.6277 (t60) outliers start: 7 outliers final: 2 residues processed: 389 average time/residue: 0.3717 time to fit residues: 219.1164 Evaluate side-chains 265 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 538 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 120 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22242 Z= 0.285 Angle : 0.675 12.154 30170 Z= 0.364 Chirality : 0.048 0.355 3112 Planarity : 0.005 0.068 3968 Dihedral : 5.420 28.099 3014 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.29 (0.16), residues: 2710 helix: -0.19 (0.19), residues: 656 sheet: 0.43 (0.17), residues: 754 loop : -0.47 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 599 HIS 0.009 0.002 HIS B 799 PHE 0.031 0.002 PHE A 178 TYR 0.055 0.002 TYR A 203 ARG 0.013 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7668 (ptm) cc_final: 0.6903 (ptt) REVERT: A 325 TYR cc_start: 0.6189 (p90) cc_final: 0.5888 (p90) REVERT: A 549 ASN cc_start: 0.8593 (t0) cc_final: 0.8299 (t0) REVERT: B 237 TYR cc_start: 0.6433 (t80) cc_final: 0.6168 (t80) REVERT: B 273 LEU cc_start: 0.7068 (tp) cc_final: 0.6413 (pt) REVERT: B 736 ILE cc_start: 0.7217 (mm) cc_final: 0.6687 (mm) REVERT: B 897 TRP cc_start: 0.6693 (t-100) cc_final: 0.6434 (t60) REVERT: C 152 MET cc_start: 0.7234 (ptm) cc_final: 0.6809 (ptm) REVERT: D 273 LEU cc_start: 0.7427 (tp) cc_final: 0.6911 (pt) REVERT: D 370 GLU cc_start: 0.6769 (tt0) cc_final: 0.6330 (tt0) REVERT: D 388 ILE cc_start: 0.8660 (mm) cc_final: 0.8392 (mm) REVERT: D 481 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7745 (tt0) REVERT: D 502 ARG cc_start: 0.5690 (tmm160) cc_final: 0.5077 (tmm160) REVERT: D 897 TRP cc_start: 0.7119 (t-100) cc_final: 0.6378 (t60) outliers start: 2 outliers final: 2 residues processed: 350 average time/residue: 0.3420 time to fit residues: 184.4326 Evaluate side-chains 246 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 180 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN D 501 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN D 933 ASN ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.8567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 22242 Z= 0.203 Angle : 0.611 12.790 30170 Z= 0.325 Chirality : 0.045 0.203 3112 Planarity : 0.004 0.075 3968 Dihedral : 5.069 29.318 3014 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.16 (0.16), residues: 2710 helix: -0.06 (0.19), residues: 674 sheet: 0.45 (0.17), residues: 764 loop : -0.37 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 599 HIS 0.004 0.001 HIS D 799 PHE 0.023 0.002 PHE A 178 TYR 0.020 0.001 TYR B 261 ARG 0.007 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7493 (ptm) cc_final: 0.6933 (ptt) REVERT: A 325 TYR cc_start: 0.6045 (p90) cc_final: 0.5790 (p90) REVERT: B 237 TYR cc_start: 0.6310 (t80) cc_final: 0.5957 (t80) REVERT: B 273 LEU cc_start: 0.7101 (tp) cc_final: 0.6500 (pt) REVERT: B 329 LYS cc_start: 0.8026 (tptp) cc_final: 0.7748 (tptt) REVERT: B 339 PHE cc_start: 0.7814 (t80) cc_final: 0.6992 (t80) REVERT: B 370 GLU cc_start: 0.6972 (tt0) cc_final: 0.6741 (tt0) REVERT: B 388 ILE cc_start: 0.8317 (mm) cc_final: 0.8088 (mm) REVERT: B 736 ILE cc_start: 0.7044 (mm) cc_final: 0.6761 (mm) REVERT: B 841 ASN cc_start: 0.7197 (p0) cc_final: 0.6993 (p0) REVERT: C 152 MET cc_start: 0.7612 (ptm) cc_final: 0.7266 (ptm) REVERT: D 273 LEU cc_start: 0.7377 (tp) cc_final: 0.6879 (pt) REVERT: D 388 ILE cc_start: 0.8695 (mm) cc_final: 0.8369 (mm) REVERT: D 507 ILE cc_start: 0.8381 (pt) cc_final: 0.8114 (pt) REVERT: D 529 LEU cc_start: 0.7975 (mt) cc_final: 0.7482 (pt) REVERT: D 897 TRP cc_start: 0.7107 (t-100) cc_final: 0.6477 (t60) outliers start: 1 outliers final: 1 residues processed: 319 average time/residue: 0.3331 time to fit residues: 167.6224 Evaluate side-chains 243 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 GLN D 501 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 933 ASN ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.9209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 22242 Z= 0.239 Angle : 0.621 11.021 30170 Z= 0.330 Chirality : 0.045 0.191 3112 Planarity : 0.004 0.043 3968 Dihedral : 5.061 30.859 3014 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.24 (0.16), residues: 2710 helix: 0.07 (0.20), residues: 676 sheet: 0.30 (0.18), residues: 764 loop : -0.46 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 897 HIS 0.006 0.001 HIS B 799 PHE 0.013 0.002 PHE C 178 TYR 0.022 0.001 TYR C 261 ARG 0.011 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 312 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.3823 (ttt) cc_final: 0.2346 (mmp) REVERT: A 152 MET cc_start: 0.7690 (ptm) cc_final: 0.6809 (ptm) REVERT: A 413 MET cc_start: 0.7412 (mmm) cc_final: 0.6019 (ttm) REVERT: B 237 TYR cc_start: 0.6557 (t80) cc_final: 0.6353 (t80) REVERT: B 273 LEU cc_start: 0.7354 (tp) cc_final: 0.6489 (pt) REVERT: B 529 LEU cc_start: 0.7977 (mp) cc_final: 0.7638 (pt) REVERT: C 152 MET cc_start: 0.7609 (ptm) cc_final: 0.7251 (ptm) REVERT: D 273 LEU cc_start: 0.7435 (tp) cc_final: 0.6970 (pt) REVERT: D 370 GLU cc_start: 0.6937 (tt0) cc_final: 0.6678 (tt0) REVERT: D 388 ILE cc_start: 0.8769 (mm) cc_final: 0.8483 (mm) REVERT: D 502 ARG cc_start: 0.5848 (tmm160) cc_final: 0.5583 (tmm160) REVERT: D 529 LEU cc_start: 0.8139 (mt) cc_final: 0.7626 (pt) outliers start: 2 outliers final: 0 residues processed: 314 average time/residue: 0.3271 time to fit residues: 162.9865 Evaluate side-chains 231 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 GLN B 864 ASN ** B 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 22242 Z= 0.477 Angle : 0.900 20.803 30170 Z= 0.479 Chirality : 0.054 0.289 3112 Planarity : 0.006 0.084 3968 Dihedral : 6.462 37.461 3014 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.92 (0.15), residues: 2710 helix: -0.69 (0.19), residues: 660 sheet: 0.32 (0.18), residues: 712 loop : -1.03 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 897 HIS 0.016 0.004 HIS A 343 PHE 0.030 0.003 PHE D1000 TYR 0.034 0.003 TYR C 354 ARG 0.010 0.001 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7900 (ptm) cc_final: 0.7312 (ptm) REVERT: A 445 MET cc_start: 0.7627 (tmm) cc_final: 0.7165 (tmm) REVERT: B 273 LEU cc_start: 0.7484 (tp) cc_final: 0.7018 (pt) REVERT: B 289 PRO cc_start: 0.7828 (Cg_exo) cc_final: 0.7336 (Cg_endo) REVERT: B 516 ASP cc_start: 0.8311 (m-30) cc_final: 0.8109 (m-30) REVERT: B 722 MET cc_start: 0.7697 (mtm) cc_final: 0.7481 (mtm) REVERT: C 269 TRP cc_start: 0.7144 (t60) cc_final: 0.6870 (t60) REVERT: D 273 LEU cc_start: 0.7606 (tp) cc_final: 0.7092 (pt) REVERT: D 388 ILE cc_start: 0.8722 (mm) cc_final: 0.8410 (tp) REVERT: D 502 ARG cc_start: 0.6210 (tmm160) cc_final: 0.5966 (tmm160) REVERT: D 516 ASP cc_start: 0.8224 (m-30) cc_final: 0.7959 (m-30) REVERT: D 525 ASP cc_start: 0.8207 (t0) cc_final: 0.7915 (t0) REVERT: D 929 ARG cc_start: 0.6430 (ttt180) cc_final: 0.5515 (tpm170) REVERT: D 935 GLU cc_start: 0.5138 (mp0) cc_final: 0.4360 (mp0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3521 time to fit residues: 166.4003 Evaluate side-chains 214 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 401 ASN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 1.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 22242 Z= 0.255 Angle : 0.659 16.620 30170 Z= 0.351 Chirality : 0.046 0.249 3112 Planarity : 0.004 0.045 3968 Dihedral : 5.553 36.775 3014 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.55 (0.16), residues: 2710 helix: -0.13 (0.20), residues: 662 sheet: 0.32 (0.18), residues: 730 loop : -0.82 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 897 HIS 0.007 0.001 HIS D 822 PHE 0.041 0.002 PHE C 178 TYR 0.041 0.002 TYR C 203 ARG 0.015 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.3829 (ttt) cc_final: 0.2650 (mmp) REVERT: A 152 MET cc_start: 0.7857 (ptm) cc_final: 0.7300 (ptm) REVERT: A 445 MET cc_start: 0.7633 (tmm) cc_final: 0.7262 (tmm) REVERT: A 454 TYR cc_start: 0.1624 (m-80) cc_final: 0.1349 (m-80) REVERT: B 427 MET cc_start: 0.8440 (mtm) cc_final: 0.8230 (ttp) REVERT: B 841 ASN cc_start: 0.7470 (p0) cc_final: 0.7100 (p0) REVERT: B 905 LEU cc_start: 0.8200 (mt) cc_final: 0.7612 (mt) REVERT: C 111 MET cc_start: 0.4416 (ptm) cc_final: 0.3928 (mmp) REVERT: C 255 MET cc_start: 0.7072 (ptm) cc_final: 0.6863 (ptm) REVERT: D 237 TYR cc_start: 0.7943 (t80) cc_final: 0.7655 (t80) REVERT: D 273 LEU cc_start: 0.7543 (tp) cc_final: 0.7030 (pt) REVERT: D 525 ASP cc_start: 0.8321 (t0) cc_final: 0.8066 (t0) REVERT: D 529 LEU cc_start: 0.8107 (mt) cc_final: 0.7487 (pt) REVERT: D 929 ARG cc_start: 0.7110 (ttt180) cc_final: 0.5643 (tpm170) REVERT: D 1013 ASN cc_start: 0.8224 (m110) cc_final: 0.7936 (t0) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3385 time to fit residues: 163.0333 Evaluate side-chains 232 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 1.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 22242 Z= 0.419 Angle : 0.818 18.518 30170 Z= 0.432 Chirality : 0.051 0.278 3112 Planarity : 0.005 0.069 3968 Dihedral : 6.103 35.137 3014 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -0.88 (0.16), residues: 2710 helix: -0.47 (0.20), residues: 658 sheet: 0.28 (0.18), residues: 726 loop : -1.09 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 599 HIS 0.014 0.003 HIS A 343 PHE 0.030 0.003 PHE C 342 TYR 0.047 0.003 TYR C 203 ARG 0.009 0.001 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8635 (mt) cc_final: 0.8405 (tt) REVERT: A 152 MET cc_start: 0.8069 (ptm) cc_final: 0.7661 (ptm) REVERT: A 413 MET cc_start: 0.7257 (mmm) cc_final: 0.6273 (ttm) REVERT: A 445 MET cc_start: 0.7671 (tmm) cc_final: 0.7392 (tmm) REVERT: A 476 MET cc_start: 0.6581 (mmp) cc_final: 0.5823 (mmp) REVERT: B 516 ASP cc_start: 0.8295 (m-30) cc_final: 0.8083 (m-30) REVERT: B 722 MET cc_start: 0.7421 (mtm) cc_final: 0.7134 (mtm) REVERT: B 841 ASN cc_start: 0.8066 (p0) cc_final: 0.7629 (p0) REVERT: B 968 MET cc_start: 0.3503 (pmm) cc_final: 0.3300 (pmm) REVERT: C 75 GLU cc_start: 0.7998 (tt0) cc_final: 0.7779 (tt0) REVERT: C 116 TYR cc_start: 0.6659 (t80) cc_final: 0.6229 (t80) REVERT: C 255 MET cc_start: 0.6971 (ptm) cc_final: 0.6676 (ptm) REVERT: C 476 MET cc_start: 0.6761 (mmp) cc_final: 0.6548 (mmp) REVERT: D 237 TYR cc_start: 0.7858 (t80) cc_final: 0.7529 (t80) REVERT: D 273 LEU cc_start: 0.7740 (tp) cc_final: 0.7172 (pt) REVERT: D 388 ILE cc_start: 0.8683 (mm) cc_final: 0.8390 (tp) REVERT: D 502 ARG cc_start: 0.5997 (tmm160) cc_final: 0.4533 (tmm160) REVERT: D 516 ASP cc_start: 0.8152 (m-30) cc_final: 0.7903 (m-30) REVERT: D 529 LEU cc_start: 0.7960 (mt) cc_final: 0.7383 (pp) REVERT: D 599 TRP cc_start: 0.2998 (t-100) cc_final: 0.2448 (t-100) REVERT: D 775 ILE cc_start: 0.6159 (mt) cc_final: 0.5697 (tt) REVERT: D 924 ILE cc_start: 0.8792 (mm) cc_final: 0.8586 (mm) REVERT: D 976 TYR cc_start: 0.6591 (p90) cc_final: 0.6390 (p90) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3241 time to fit residues: 139.8963 Evaluate side-chains 209 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 1.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 22242 Z= 0.415 Angle : 0.801 18.319 30170 Z= 0.425 Chirality : 0.051 0.293 3112 Planarity : 0.005 0.073 3968 Dihedral : 6.097 36.103 3014 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.04 (0.15), residues: 2710 helix: -0.72 (0.19), residues: 668 sheet: 0.22 (0.18), residues: 722 loop : -1.13 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 897 HIS 0.011 0.002 HIS D 799 PHE 0.037 0.003 PHE C 178 TYR 0.037 0.002 TYR C 203 ARG 0.035 0.001 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4374 (ptm) cc_final: 0.3334 (mmm) REVERT: A 152 MET cc_start: 0.8144 (ptm) cc_final: 0.7578 (ptm) REVERT: A 413 MET cc_start: 0.7261 (mmm) cc_final: 0.6696 (ttm) REVERT: A 445 MET cc_start: 0.7683 (tmm) cc_final: 0.7393 (tmm) REVERT: B 485 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8248 (mttm) REVERT: B 841 ASN cc_start: 0.7933 (p0) cc_final: 0.7517 (p0) REVERT: C 111 MET cc_start: 0.4950 (ptm) cc_final: 0.4494 (mmp) REVERT: C 465 LEU cc_start: 0.7564 (mm) cc_final: 0.7081 (tp) REVERT: C 476 MET cc_start: 0.6768 (mmp) cc_final: 0.6541 (mmp) REVERT: D 237 TYR cc_start: 0.8007 (t80) cc_final: 0.7652 (t80) REVERT: D 273 LEU cc_start: 0.7830 (tp) cc_final: 0.7289 (pt) REVERT: D 502 ARG cc_start: 0.6090 (tmm160) cc_final: 0.4783 (tmm160) REVERT: D 525 ASP cc_start: 0.8166 (t0) cc_final: 0.7792 (t0) REVERT: D 772 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6542 (ttp80) REVERT: D 929 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6588 (ttt90) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3587 time to fit residues: 151.7657 Evaluate side-chains 213 residues out of total 2294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 59 optimal weight: 0.0970 chunk 214 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.134880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113338 restraints weight = 53763.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112138 restraints weight = 85013.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113005 restraints weight = 75950.122| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 1.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 22242 Z= 0.239 Angle : 0.664 16.277 30170 Z= 0.353 Chirality : 0.047 0.237 3112 Planarity : 0.004 0.056 3968 Dihedral : 5.527 36.469 3014 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2710 helix: -0.39 (0.19), residues: 674 sheet: 0.15 (0.18), residues: 744 loop : -0.96 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 486 HIS 0.009 0.001 HIS D 822 PHE 0.019 0.002 PHE A 342 TYR 0.026 0.001 TYR C 203 ARG 0.009 0.001 ARG D 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.79 seconds wall clock time: 80 minutes 26.89 seconds (4826.89 seconds total)