Starting phenix.real_space_refine on Fri Mar 22 12:30:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zm1_11277/03_2024/6zm1_11277.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10980 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 79 5.16 5 C 14254 2.51 5 N 3810 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 615": "OD1" <-> "OD2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ASP 885": "OD1" <-> "OD2" Residue "B PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 22543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} 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: 11.24, per 1000 atoms: 0.50 Number of scatterers: 22543 At special positions: 0 Unit cell: (142.31, 148.73, 131.61, 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 79 16.00 O 4400 8.00 N 3810 7.00 C 14254 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=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.05 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: 8.61 Conformation dependent library (CDL) restraints added in 3.6 seconds 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5176 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 25.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.737A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.333A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.907A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.909A pdb=" N HIS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.676A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.548A pdb=" N ILE A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP B 96 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.813A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.596A pdb=" N ASN B 913 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.993A 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: 4.556A 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: 3.574A 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: 3.940A 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: 3.652A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 4.044A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.654A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.801A 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: 3.550A pdb=" N LEU C 258 " --> pdb=" O MET C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.597A 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: 3.736A 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: 4.515A pdb=" N SER C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.889A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.784A 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: 3.524A 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: 5.987A 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: 3.521A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.713A 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: 3.868A 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= A, first strand: chain 'A' and resid 269 through 271 removed outlier: 4.075A pdb=" N TRP A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 405 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 271 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE A 403 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.364A pdb=" N ILE B 179 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 178 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 156 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE B 202 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 158 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 157 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 162 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 128 through 132 Processing sheet with id= E, first strand: chain 'B' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR B 327 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 304 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 305 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 218 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1012 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 220 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 953 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 873 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 745 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 711 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 749 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 706 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 712 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 627 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 617 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 574 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 514 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 554 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 508 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 506 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 509 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B 488 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 221 through 224 Processing sheet with id= G, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG B 345 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.703A pdb=" N ARG B 426 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 452 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS B 482 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS B 518 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA B 475 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE B 736 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 879 through 881 Processing sheet with id= L, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.803A pdb=" N GLY B 264 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 273 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.605A pdb=" N GLU B 777 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 742 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE B 775 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 744 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 773 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR B 853 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 806 " --> pdb=" O TRP B 851 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP B 851 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= P, first strand: chain 'D' and resid 302 through 312 removed outlier: 3.581A pdb=" N ARG D 972 " --> pdb=" O GLY D1015 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE D 877 " --> pdb=" O ARG D 952 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D 954 " --> pdb=" O THR D 875 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 875 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU D 956 " --> pdb=" O ASP D 873 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP D 873 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA D 740 " --> pdb=" O LEU D 776 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 457 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG D 421 " --> pdb=" O ARG D 457 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 719 through 722 Processing sheet with id= R, first strand: chain 'D' and resid 765 through 769 Processing sheet with id= S, first strand: chain 'D' and resid 885 through 887 Processing sheet with id= T, first strand: chain 'D' and resid 948 through 951 removed outlier: 4.268A pdb=" N LEU D 983 " --> pdb=" O LEU D 951 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.706A pdb=" N GLY D 264 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU D 273 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 638 through 640 removed outlier: 3.708A pdb=" N GLN D 677 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA D 640 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG D 675 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 804 through 807 removed outlier: 6.361A pdb=" N GLY D 806 " --> pdb=" O TRP D 851 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP D 851 " --> pdb=" O GLY D 806 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2475 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: 8.26 Time building geometry restraints manager: 9.40 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: 7388 1.34 - 1.47: 6151 1.47 - 1.60: 9413 1.60 - 1.73: 0 1.73 - 1.86: 140 Bond restraints: 23092 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 7.23e+00 bond pdb=" CB ASN D 785 " pdb=" CG ASN D 785 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.03e+00 bond pdb=" CB ASP D 292 " pdb=" CG ASP D 292 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" C THR D 469 " pdb=" N ASN D 470 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.55e-02 4.16e+03 3.47e+00 bond pdb=" CG GLN C 197 " pdb=" CD GLN C 197 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.34e+00 ... (remaining 23087 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.68: 386 105.68 - 112.79: 11216 112.79 - 119.91: 8453 119.91 - 127.02: 11016 127.02 - 134.14: 269 Bond angle restraints: 31340 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 113.60 122.40 -8.80 1.90e+00 2.77e-01 2.14e+01 angle pdb=" C CYS A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta sigma weight residual 121.70 129.30 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" C GLY B 167 " pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C ASP A 388 " pdb=" N CYS A 389 " pdb=" CA CYS A 389 " ideal model delta sigma weight residual 120.28 126.18 -5.90 1.44e+00 4.82e-01 1.68e+01 angle pdb=" C LEU A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 31335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11882 17.85 - 35.70: 1228 35.70 - 53.55: 277 53.55 - 71.41: 65 71.41 - 89.26: 36 Dihedral angle restraints: 13488 sinusoidal: 5289 harmonic: 8199 Sorted by residual: 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 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA CYS A 387 " pdb=" C CYS A 387 " pdb=" N ASP A 388 " pdb=" CA ASP A 388 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+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 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 13485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2843 0.080 - 0.160: 395 0.160 - 0.239: 20 0.239 - 0.319: 4 0.319 - 0.399: 1 Chirality restraints: 3263 Sorted by residual: 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 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE B 212 " pdb=" CA ILE B 212 " pdb=" CG1 ILE B 212 " pdb=" CG2 ILE B 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL B 668 " pdb=" CA VAL B 668 " pdb=" CG1 VAL B 668 " pdb=" CG2 VAL B 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3260 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 384 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+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 " 0.041 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 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 826 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLU B 826 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 826 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 826 " 0.013 2.00e-02 2.50e+03 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.64: 11 1.64 - 2.46: 165 2.46 - 3.27: 23367 3.27 - 4.09: 57122 4.09 - 4.90: 104687 Warning: very small nonbonded interaction distances. Nonbonded interactions: 185352 Sorted by model distance: nonbonded pdb=" O GLY B 547 " pdb=" OD2 ASP D 537 " model vdw 0.828 3.040 nonbonded pdb=" O VAL C 14 " pdb=" N TYR D 639 " model vdw 1.047 2.520 nonbonded pdb=" CD LYS C 370 " pdb=" CB ALA D 256 " model vdw 1.063 3.860 nonbonded pdb=" CD1 PHE C 536 " pdb=" OE2 GLU D 846 " model vdw 1.078 3.340 nonbonded pdb=" NH1 ARG C 7 " pdb=" NH2 ARG D 513 " model vdw 1.104 3.200 ... (remaining 185347 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' and (resid 1 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 141 or (resid 142 and (name N or na \ me CA or name C or name O or name CB )) or resid 143 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 254 \ or (resid 255 and (name N or name CA or name C or name O or name CB )) or resid \ 256 through 312 or (resid 313 and (name N or name CA or name C or name O or nam \ e CB )) or resid 314 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 329 or (resid 330 and (name N or na \ me CA or name C or name O or name CB )) or resid 331 through 335 or (resid 336 a \ nd (name N or name CA or name C or name O or name CB )) or resid 337 through 352 \ or (resid 353 and (name N or name CA or name C or name O or name CB )) or resid \ 354 through 391 or (resid 392 and (name N or name CA or name C or name O or nam \ e CB )) or resid 393 through 422 or (resid 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 through 429 or (resid 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 444 or (resid 445 a \ nd (name N or name CA or name C or name O or name CB )) or resid 446 through 449 \ or (resid 450 and (name N or name CA or name C or name O or name CB )) or resid \ 451 or (resid 452 and (name N or name CA or name C or name O or name CB )) or r \ esid 453 through 471 or (resid 472 through 473 and (name N or name CA or name C \ or name O or name CB )) or resid 474 or (resid 475 through 476 and (name N or na \ me CA or name C or name O or name CB )) or resid 477 through 501 or (resid 502 a \ nd (name N or name CA or name C or name O or name CB )) or resid 503 through 511 \ or (resid 512 through 513 and (name N or name CA or name C or name O or name CB \ )) or resid 514 through 519 or (resid 520 and (name N or name CA or name C or n \ ame O or name CB )) or resid 521 through 552)) } ncs_group { reference = (chain 'B' and resid 213 through 1016) 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 5.330 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 58.420 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 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 : 0.007 0.067 23092 Z= 0.438 Angle : 0.907 9.625 31340 Z= 0.510 Chirality : 0.055 0.399 3263 Planarity : 0.006 0.074 4129 Dihedral : 16.150 89.256 8300 Min Nonbonded Distance : 0.828 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.49 % Favored : 93.30 % Rotamer: Outliers : 0.55 % Allowed : 15.28 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -3.15 (0.14), residues: 2836 helix: -2.69 (0.15), residues: 623 sheet: -1.56 (0.18), residues: 741 loop : -2.05 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 425 HIS 0.009 0.002 HIS D 362 PHE 0.026 0.003 PHE D 942 TYR 0.027 0.003 TYR B 422 ARG 0.008 0.001 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 510 time to evaluate : 2.815 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: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 450 ASP cc_start: 0.5995 (t70) cc_final: 0.5697 (t70) REVERT: B 480 GLN cc_start: 0.8208 (tp40) cc_final: 0.7988 (tt0) REVERT: B 487 MET cc_start: 0.7673 (ptm) cc_final: 0.7467 (ptm) REVERT: B 489 ASN cc_start: 0.5012 (p0) cc_final: 0.4723 (p0) REVERT: B 507 ILE cc_start: 0.8098 (pt) cc_final: 0.7688 (tt) REVERT: B 526 PHE cc_start: 0.8433 (m-80) cc_final: 0.8111 (m-10) REVERT: B 630 ILE cc_start: 0.8576 (pt) cc_final: 0.8019 (mp) REVERT: B 948 PHE cc_start: 0.7256 (p90) cc_final: 0.6747 (p90) REVERT: C 50 ASN cc_start: 0.8069 (m110) cc_final: 0.7867 (m-40) REVERT: C 57 ASP cc_start: 0.8526 (m-30) cc_final: 0.7985 (t0) REVERT: C 97 CYS cc_start: 0.7408 (m) cc_final: 0.7198 (m) REVERT: C 160 LEU cc_start: 0.7176 (mt) cc_final: 0.6823 (mt) REVERT: C 276 ASN cc_start: 0.7525 (m-40) cc_final: 0.7300 (m-40) REVERT: C 284 LEU cc_start: 0.9281 (mt) cc_final: 0.8935 (mp) REVERT: C 312 PHE cc_start: 0.7743 (m-80) cc_final: 0.7250 (m-10) REVERT: C 412 LEU cc_start: 0.7710 (mt) cc_final: 0.7505 (mt) REVERT: C 450 TYR cc_start: 0.6682 (m-10) cc_final: 0.6269 (m-10) REVERT: C 485 PHE cc_start: 0.7516 (m-80) cc_final: 0.6873 (m-10) REVERT: D 234 THR cc_start: 0.8142 (m) cc_final: 0.7810 (p) REVERT: D 293 THR cc_start: 0.8049 (m) cc_final: 0.6681 (p) REVERT: D 414 LEU cc_start: 0.8611 (mt) cc_final: 0.8403 (mp) REVERT: D 450 ASP cc_start: 0.7421 (t0) cc_final: 0.6978 (t70) REVERT: D 470 ASN cc_start: 0.6164 (t0) cc_final: 0.5890 (t0) REVERT: D 487 MET cc_start: 0.7662 (tmm) cc_final: 0.6198 (tmm) REVERT: D 669 LEU cc_start: 0.8779 (mt) cc_final: 0.8445 (mp) REVERT: D 867 LEU cc_start: 0.8010 (mt) cc_final: 0.7197 (mm) REVERT: D 954 ILE cc_start: 0.6990 (tt) cc_final: 0.5048 (tt) outliers start: 13 outliers final: 2 residues processed: 519 average time/residue: 0.3795 time to fit residues: 300.6948 Evaluate side-chains 261 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 0.0570 chunk 134 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 134 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 422 ASN A 506 ASN A 538 GLN B 122 GLN B 174 ASN B 266 ASN B 362 HIS B 434 ASN B 501 HIS B 628 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B 816 GLN B 849 GLN B 919 ASN C 43 ASN C 50 ASN C 256 ASN C 263 ASN C 272 GLN C 401 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 306 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 GLN ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 ASN D 980 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 23092 Z= 0.246 Angle : 0.654 8.597 31340 Z= 0.358 Chirality : 0.045 0.176 3263 Planarity : 0.005 0.075 4129 Dihedral : 5.437 31.261 3146 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 0.25 % Allowed : 4.76 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.82 (0.15), residues: 2836 helix: -0.83 (0.19), residues: 649 sheet: -0.87 (0.19), residues: 733 loop : -1.51 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 498 HIS 0.008 0.002 HIS D 362 PHE 0.046 0.002 PHE C 178 TYR 0.032 0.002 TYR C 203 ARG 0.015 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 2.584 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: A 288 MET cc_start: 0.7491 (tmm) cc_final: 0.7159 (tmm) REVERT: A 474 MET cc_start: 0.7380 (mmt) cc_final: 0.6914 (mmt) REVERT: B 118 VAL cc_start: 0.8176 (t) cc_final: 0.7925 (t) REVERT: B 276 MET cc_start: 0.4003 (tpt) cc_final: 0.3567 (tpt) REVERT: B 336 ASP cc_start: 0.7957 (m-30) cc_final: 0.7707 (t0) REVERT: B 347 ASN cc_start: 0.7894 (m-40) cc_final: 0.7557 (m110) REVERT: B 480 GLN cc_start: 0.7429 (tp40) cc_final: 0.7182 (tt0) REVERT: B 485 LYS cc_start: 0.7091 (tttt) cc_final: 0.6034 (tttt) REVERT: B 530 THR cc_start: 0.7460 (p) cc_final: 0.7002 (m) REVERT: C 35 ILE cc_start: 0.8082 (tp) cc_final: 0.7514 (tp) REVERT: C 129 LEU cc_start: 0.9077 (mt) cc_final: 0.8649 (mp) REVERT: C 152 MET cc_start: 0.7577 (ttt) cc_final: 0.7150 (ttt) REVERT: C 237 THR cc_start: 0.7459 (p) cc_final: 0.7200 (p) REVERT: C 277 ASP cc_start: 0.4344 (p0) cc_final: 0.3692 (p0) REVERT: C 284 LEU cc_start: 0.9446 (mt) cc_final: 0.9245 (mp) REVERT: C 347 MET cc_start: 0.6599 (mpp) cc_final: 0.6286 (mpp) REVERT: C 412 LEU cc_start: 0.7677 (mt) cc_final: 0.7466 (mt) REVERT: C 450 TYR cc_start: 0.7468 (m-10) cc_final: 0.6939 (m-80) REVERT: C 474 MET cc_start: 0.7260 (mmm) cc_final: 0.6932 (mmm) REVERT: C 487 MET cc_start: 0.9034 (mmm) cc_final: 0.8593 (mmm) REVERT: D 300 THR cc_start: 0.7487 (t) cc_final: 0.7233 (t) REVERT: D 368 THR cc_start: 0.6377 (m) cc_final: 0.5165 (p) REVERT: D 630 ILE cc_start: 0.7904 (pt) cc_final: 0.7269 (pt) REVERT: D 669 LEU cc_start: 0.8273 (mt) cc_final: 0.7882 (mm) REVERT: D 865 ILE cc_start: 0.7433 (pt) cc_final: 0.7065 (mp) outliers start: 6 outliers final: 3 residues processed: 313 average time/residue: 0.3456 time to fit residues: 167.5600 Evaluate side-chains 207 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 255 optimal weight: 8.9990 chunk 87 optimal weight: 0.0770 chunk 206 optimal weight: 20.0000 overall best weight: 5.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 50 ASN A 72 ASN A 88 ASN A 167 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN B 366 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 945 ASN C 256 ASN C 260 GLN C 327 ASN ** C 538 GLN ** 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 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS ** D 677 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 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 23092 Z= 0.371 Angle : 0.733 11.733 31340 Z= 0.398 Chirality : 0.046 0.188 3263 Planarity : 0.005 0.097 4129 Dihedral : 5.675 32.869 3146 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.52 (0.15), residues: 2836 helix: -0.42 (0.20), residues: 643 sheet: -0.72 (0.19), residues: 744 loop : -1.39 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 599 HIS 0.008 0.002 HIS A 132 PHE 0.030 0.002 PHE D 459 TYR 0.025 0.002 TYR D 461 ARG 0.008 0.001 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 2.846 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 474 MET cc_start: 0.7432 (mmt) cc_final: 0.7138 (mmt) REVERT: A 487 MET cc_start: 0.8270 (pmm) cc_final: 0.7952 (pmm) REVERT: B 170 GLU cc_start: 0.7667 (pm20) cc_final: 0.7206 (pm20) REVERT: B 276 MET cc_start: 0.4228 (tpt) cc_final: 0.3800 (tpt) REVERT: B 512 ASN cc_start: 0.6968 (t0) cc_final: 0.6766 (t0) REVERT: B 948 PHE cc_start: 0.7447 (p90) cc_final: 0.7109 (p90) REVERT: C 60 LYS cc_start: 0.7679 (pttm) cc_final: 0.7403 (pttp) REVERT: C 174 ILE cc_start: 0.8902 (mm) cc_final: 0.8163 (tp) REVERT: C 412 LEU cc_start: 0.7807 (mt) cc_final: 0.7593 (mt) REVERT: C 474 MET cc_start: 0.7498 (mmm) cc_final: 0.7073 (mmm) REVERT: C 516 CYS cc_start: 0.7580 (t) cc_final: 0.6973 (m) REVERT: D 349 ASP cc_start: 0.7846 (t0) cc_final: 0.7435 (t0) REVERT: D 422 TYR cc_start: 0.8271 (p90) cc_final: 0.8002 (p90) REVERT: D 449 LEU cc_start: 0.8138 (tt) cc_final: 0.7886 (tt) REVERT: D 463 TYR cc_start: 0.6715 (p90) cc_final: 0.6437 (p90) REVERT: D 833 ILE cc_start: 0.8110 (mt) cc_final: 0.7542 (mm) REVERT: D 865 ILE cc_start: 0.7487 (pt) cc_final: 0.7138 (pt) outliers start: 3 outliers final: 2 residues processed: 229 average time/residue: 0.3455 time to fit residues: 126.4499 Evaluate side-chains 168 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 628 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 302 HIS ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 23092 Z= 0.311 Angle : 0.670 11.552 31340 Z= 0.361 Chirality : 0.045 0.179 3263 Planarity : 0.005 0.059 4129 Dihedral : 5.459 34.812 3146 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.26 (0.15), residues: 2836 helix: -0.07 (0.20), residues: 643 sheet: -0.62 (0.19), residues: 735 loop : -1.25 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 735 HIS 0.013 0.002 HIS D 362 PHE 0.028 0.002 PHE C 350 TYR 0.033 0.002 TYR C 203 ARG 0.007 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.7429 (mmt) cc_final: 0.7196 (mmt) REVERT: B 276 MET cc_start: 0.4149 (tpt) cc_final: 0.3529 (tpt) REVERT: C 60 LYS cc_start: 0.8041 (pttm) cc_final: 0.7647 (pttp) REVERT: C 129 LEU cc_start: 0.9026 (mp) cc_final: 0.8772 (mt) REVERT: C 412 LEU cc_start: 0.7742 (mt) cc_final: 0.7525 (mt) REVERT: C 413 MET cc_start: 0.9138 (ptm) cc_final: 0.8802 (ptm) REVERT: C 474 MET cc_start: 0.7311 (mmm) cc_final: 0.6931 (mmm) REVERT: C 487 MET cc_start: 0.8760 (mmm) cc_final: 0.8548 (mtt) REVERT: C 516 CYS cc_start: 0.8009 (t) cc_final: 0.7512 (m) REVERT: D 217 ASP cc_start: 0.8093 (m-30) cc_final: 0.7281 (t0) REVERT: D 349 ASP cc_start: 0.8166 (t0) cc_final: 0.7841 (t0) REVERT: D 427 MET cc_start: 0.8473 (mpp) cc_final: 0.8113 (mtt) REVERT: D 449 LEU cc_start: 0.7873 (tt) cc_final: 0.7552 (tt) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.3382 time to fit residues: 112.9811 Evaluate side-chains 154 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 69 optimal weight: 0.0370 overall best weight: 2.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN C 151 ASN C 220 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23092 Z= 0.201 Angle : 0.593 14.456 31340 Z= 0.316 Chirality : 0.044 0.207 3263 Planarity : 0.004 0.050 4129 Dihedral : 5.030 34.206 3146 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2836 helix: 0.36 (0.21), residues: 628 sheet: -0.49 (0.19), residues: 725 loop : -1.07 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 535 HIS 0.008 0.001 HIS A 132 PHE 0.024 0.001 PHE D 948 TYR 0.019 0.001 TYR A 157 ARG 0.005 0.000 ARG D 675 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 2.526 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: B 276 MET cc_start: 0.3775 (tpt) cc_final: 0.3025 (tpt) REVERT: B 336 ASP cc_start: 0.7364 (t0) cc_final: 0.7123 (t70) REVERT: B 347 ASN cc_start: 0.7734 (p0) cc_final: 0.7319 (p0) REVERT: B 480 GLN cc_start: 0.6975 (tp40) cc_final: 0.5987 (tt0) REVERT: B 485 LYS cc_start: 0.6658 (tttt) cc_final: 0.6254 (tttp) REVERT: B 948 PHE cc_start: 0.7389 (p90) cc_final: 0.7135 (p90) REVERT: C 412 LEU cc_start: 0.7616 (mt) cc_final: 0.7371 (mt) REVERT: C 474 MET cc_start: 0.7274 (mmm) cc_final: 0.7036 (mmm) REVERT: C 487 MET cc_start: 0.8739 (mmm) cc_final: 0.8055 (mtp) REVERT: D 217 ASP cc_start: 0.7885 (m-30) cc_final: 0.7219 (t0) REVERT: D 347 ASN cc_start: 0.8667 (m-40) cc_final: 0.8260 (m-40) REVERT: D 349 ASP cc_start: 0.8197 (t0) cc_final: 0.7749 (t0) REVERT: D 696 ASP cc_start: 0.5305 (p0) cc_final: 0.4934 (p0) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.3180 time to fit residues: 107.7613 Evaluate side-chains 157 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 67 optimal weight: 0.0040 chunk 273 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 4.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 139 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 495 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23092 Z= 0.291 Angle : 0.645 10.949 31340 Z= 0.347 Chirality : 0.044 0.180 3263 Planarity : 0.004 0.069 4129 Dihedral : 5.230 35.076 3146 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2836 helix: 0.24 (0.21), residues: 636 sheet: -0.56 (0.19), residues: 729 loop : -1.13 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 599 HIS 0.005 0.001 HIS A 132 PHE 0.034 0.002 PHE C 178 TYR 0.028 0.002 TYR C 203 ARG 0.017 0.001 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 2.564 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: A 487 MET cc_start: 0.8412 (pmm) cc_final: 0.8150 (pmm) REVERT: B 276 MET cc_start: 0.4040 (tpt) cc_final: 0.3235 (tpt) REVERT: B 336 ASP cc_start: 0.7291 (t0) cc_final: 0.7037 (t70) REVERT: B 347 ASN cc_start: 0.7583 (p0) cc_final: 0.7170 (p0) REVERT: B 485 LYS cc_start: 0.6535 (tttt) cc_final: 0.6106 (tptt) REVERT: B 741 MET cc_start: 0.6335 (ttp) cc_final: 0.6023 (ttt) REVERT: B 948 PHE cc_start: 0.7309 (p90) cc_final: 0.7102 (p90) REVERT: C 474 MET cc_start: 0.7383 (mmm) cc_final: 0.7116 (mmm) REVERT: D 217 ASP cc_start: 0.7776 (m-30) cc_final: 0.7049 (t0) REVERT: D 347 ASN cc_start: 0.8596 (m-40) cc_final: 0.8284 (m-40) REVERT: D 349 ASP cc_start: 0.8126 (t0) cc_final: 0.7671 (t0) REVERT: D 350 TYR cc_start: 0.6385 (m-80) cc_final: 0.6042 (m-80) REVERT: D 449 LEU cc_start: 0.7910 (tt) cc_final: 0.7649 (tt) REVERT: D 534 MET cc_start: 0.8602 (mmm) cc_final: 0.8138 (mmt) REVERT: D 696 ASP cc_start: 0.5352 (p0) cc_final: 0.5118 (p0) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.3071 time to fit residues: 92.6109 Evaluate side-chains 151 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 166 optimal weight: 0.0570 chunk 125 optimal weight: 9.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS B 628 GLN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23092 Z= 0.151 Angle : 0.570 8.756 31340 Z= 0.303 Chirality : 0.044 0.203 3263 Planarity : 0.004 0.065 4129 Dihedral : 4.763 35.503 3146 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 1.31 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2836 helix: 0.54 (0.22), residues: 626 sheet: -0.41 (0.19), residues: 731 loop : -0.94 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 91 HIS 0.008 0.001 HIS A 132 PHE 0.019 0.001 PHE C 178 TYR 0.021 0.001 TYR C 203 ARG 0.004 0.000 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 2.635 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: B 169 HIS cc_start: 0.7438 (p90) cc_final: 0.7011 (p-80) REVERT: B 276 MET cc_start: 0.3726 (tpt) cc_final: 0.3062 (tpt) REVERT: B 336 ASP cc_start: 0.7340 (t0) cc_final: 0.7025 (t70) REVERT: B 347 ASN cc_start: 0.7572 (p0) cc_final: 0.7182 (p0) REVERT: B 361 GLN cc_start: 0.7934 (pp30) cc_final: 0.6581 (pp30) REVERT: B 455 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7890 (tt0) REVERT: B 485 LYS cc_start: 0.6139 (tttp) cc_final: 0.5770 (tttp) REVERT: B 741 MET cc_start: 0.6591 (ttp) cc_final: 0.6152 (ttt) REVERT: B 948 PHE cc_start: 0.7303 (p90) cc_final: 0.7039 (p90) REVERT: D 217 ASP cc_start: 0.7793 (m-30) cc_final: 0.7204 (t0) REVERT: D 347 ASN cc_start: 0.8582 (m-40) cc_final: 0.8154 (m-40) REVERT: D 349 ASP cc_start: 0.8000 (t0) cc_final: 0.7532 (p0) REVERT: D 449 LEU cc_start: 0.7989 (tt) cc_final: 0.7681 (tt) REVERT: D 451 TYR cc_start: 0.7527 (t80) cc_final: 0.6989 (t80) REVERT: D 534 MET cc_start: 0.8418 (mmm) cc_final: 0.8002 (mmt) REVERT: D 696 ASP cc_start: 0.5521 (p0) cc_final: 0.5180 (p0) REVERT: D 865 ILE cc_start: 0.8274 (pt) cc_final: 0.7891 (pt) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.3092 time to fit residues: 103.2545 Evaluate side-chains 163 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 624 GLN B 628 GLN B 642 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 420 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 23092 Z= 0.308 Angle : 0.660 10.286 31340 Z= 0.353 Chirality : 0.045 0.255 3263 Planarity : 0.004 0.058 4129 Dihedral : 5.149 35.590 3146 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.06 (0.16), residues: 2836 helix: 0.22 (0.21), residues: 633 sheet: -0.57 (0.19), residues: 713 loop : -1.14 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 91 HIS 0.007 0.001 HIS A 132 PHE 0.017 0.002 PHE D 526 TYR 0.026 0.002 TYR B 191 ARG 0.016 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.8991 (mpp) cc_final: 0.8764 (mpp) REVERT: B 276 MET cc_start: 0.3812 (tpt) cc_final: 0.3269 (tpt) REVERT: B 336 ASP cc_start: 0.7517 (t0) cc_final: 0.7175 (t70) REVERT: B 347 ASN cc_start: 0.7782 (p0) cc_final: 0.7347 (p0) REVERT: B 485 LYS cc_start: 0.6172 (tttp) cc_final: 0.5894 (tttp) REVERT: B 741 MET cc_start: 0.6678 (ttp) cc_final: 0.6322 (ttt) REVERT: B 948 PHE cc_start: 0.7333 (p90) cc_final: 0.7104 (p90) REVERT: C 487 MET cc_start: 0.9167 (mmm) cc_final: 0.8936 (mmm) REVERT: D 217 ASP cc_start: 0.7774 (m-30) cc_final: 0.7143 (t0) REVERT: D 349 ASP cc_start: 0.7988 (t0) cc_final: 0.7617 (t0) REVERT: D 350 TYR cc_start: 0.6407 (m-80) cc_final: 0.6088 (m-80) REVERT: D 449 LEU cc_start: 0.7939 (tt) cc_final: 0.7657 (tt) REVERT: D 487 MET cc_start: 0.8061 (tmm) cc_final: 0.7840 (tmm) REVERT: D 534 MET cc_start: 0.8638 (mmm) cc_final: 0.8142 (mmt) REVERT: D 696 ASP cc_start: 0.5381 (p0) cc_final: 0.5180 (p0) REVERT: D 865 ILE cc_start: 0.8204 (pt) cc_final: 0.7721 (mm) outliers start: 2 outliers final: 2 residues processed: 179 average time/residue: 0.3060 time to fit residues: 91.0014 Evaluate side-chains 153 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 ASN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 23092 Z= 0.157 Angle : 0.587 10.983 31340 Z= 0.310 Chirality : 0.045 0.273 3263 Planarity : 0.004 0.054 4129 Dihedral : 4.752 35.359 3146 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.04 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.85 (0.16), residues: 2836 helix: 0.35 (0.21), residues: 640 sheet: -0.40 (0.19), residues: 733 loop : -1.02 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 612 HIS 0.009 0.001 HIS C 302 PHE 0.025 0.001 PHE C 536 TYR 0.024 0.001 TYR B 245 ARG 0.005 0.000 ARG D 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 MET cc_start: 0.3571 (tpt) cc_final: 0.3300 (tpt) REVERT: B 336 ASP cc_start: 0.7491 (t0) cc_final: 0.7195 (t70) REVERT: B 347 ASN cc_start: 0.7703 (p0) cc_final: 0.7196 (p0) REVERT: B 361 GLN cc_start: 0.7482 (pp30) cc_final: 0.6353 (pp30) REVERT: B 741 MET cc_start: 0.6875 (ttp) cc_final: 0.6463 (ttt) REVERT: B 948 PHE cc_start: 0.7300 (p90) cc_final: 0.7019 (p90) REVERT: D 217 ASP cc_start: 0.7803 (m-30) cc_final: 0.7222 (t0) REVERT: D 347 ASN cc_start: 0.8578 (m-40) cc_final: 0.8211 (m-40) REVERT: D 349 ASP cc_start: 0.7892 (t0) cc_final: 0.7583 (p0) REVERT: D 449 LEU cc_start: 0.7897 (tt) cc_final: 0.7506 (tt) REVERT: D 451 TYR cc_start: 0.7470 (t80) cc_final: 0.7149 (t80) REVERT: D 534 MET cc_start: 0.8434 (mmm) cc_final: 0.7898 (mmt) REVERT: D 696 ASP cc_start: 0.5536 (p0) cc_final: 0.5220 (p0) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.3056 time to fit residues: 96.9078 Evaluate side-chains 159 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 86 ASN A 102 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 518 HIS ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN C 232 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN D 799 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.8468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23092 Z= 0.286 Angle : 0.667 11.806 31340 Z= 0.354 Chirality : 0.045 0.203 3263 Planarity : 0.004 0.051 4129 Dihedral : 5.118 35.002 3146 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2836 helix: 0.20 (0.20), residues: 639 sheet: -0.43 (0.19), residues: 698 loop : -1.18 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 49 HIS 0.007 0.002 HIS B 169 PHE 0.023 0.002 PHE B 526 TYR 0.025 0.002 TYR B 245 ARG 0.006 0.001 ARG D 937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.664 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: B 276 MET cc_start: 0.3755 (tpt) cc_final: 0.3456 (tpt) REVERT: B 336 ASP cc_start: 0.7637 (t0) cc_final: 0.7243 (t70) REVERT: B 347 ASN cc_start: 0.7807 (p0) cc_final: 0.7244 (p0) REVERT: B 485 LYS cc_start: 0.6270 (tttp) cc_final: 0.5962 (tptt) REVERT: B 948 PHE cc_start: 0.7303 (p90) cc_final: 0.7065 (p90) REVERT: C 152 MET cc_start: 0.6966 (ppp) cc_final: 0.6612 (ppp) REVERT: C 487 MET cc_start: 0.8996 (mmm) cc_final: 0.8114 (mtp) REVERT: D 217 ASP cc_start: 0.7748 (m-30) cc_final: 0.7135 (t0) REVERT: D 347 ASN cc_start: 0.8576 (m-40) cc_final: 0.8282 (m-40) REVERT: D 349 ASP cc_start: 0.7995 (t0) cc_final: 0.7652 (t0) REVERT: D 449 LEU cc_start: 0.8005 (tt) cc_final: 0.7708 (tt) REVERT: D 451 TYR cc_start: 0.7639 (t80) cc_final: 0.7337 (t80) REVERT: D 534 MET cc_start: 0.8634 (mmm) cc_final: 0.8142 (mmt) outliers start: 1 outliers final: 1 residues processed: 171 average time/residue: 0.3104 time to fit residues: 88.4195 Evaluate side-chains 141 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 ASN D 791 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045375 restraints weight = 140532.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045140 restraints weight = 113495.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045763 restraints weight = 88903.276| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23092 Z= 0.260 Angle : 0.638 12.020 31340 Z= 0.339 Chirality : 0.045 0.189 3263 Planarity : 0.004 0.087 4129 Dihedral : 5.103 34.956 3146 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.03 (0.16), residues: 2836 helix: 0.24 (0.21), residues: 632 sheet: -0.48 (0.19), residues: 714 loop : -1.17 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 612 HIS 0.005 0.001 HIS C 302 PHE 0.013 0.002 PHE D 526 TYR 0.023 0.002 TYR B 245 ARG 0.010 0.001 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.63 seconds wall clock time: 72 minutes 14.86 seconds (4334.86 seconds total)