Starting phenix.real_space_refine on Sun Mar 17 16:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/03_2024/6qct_4512_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11414 2.51 5 N 3150 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5793 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 26, 'TRANS': 695} Chain: "B" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5774 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 700} Chain breaks: 1 Chain: "C" Number of atoms: 5832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5832 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 284 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "R" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "M" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 313 Unusual residues: {'GTG': 1} Classifications: {'RNA': 12, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.48, per 1000 atoms: 0.52 Number of scatterers: 18266 At special positions: 0 Unit cell: (122.172, 127.989, 120.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 41 15.00 Mg 2 11.99 O 3527 8.00 N 3150 7.00 C 11414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.5 seconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 21 sheets defined 40.9% alpha, 11.8% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 8.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.921A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 128 through 138 removed outlier: 4.225A pdb=" N GLU A 137 " --> pdb=" O TRP A 133 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 430 through 446 removed outlier: 4.280A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.393A pdb=" N GLN A 579 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN A 582 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 586 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN A 595 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 629 through 645 Processing helix chain 'A' and resid 649 through 669 removed outlier: 3.990A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.813A pdb=" N ILE A 686 " --> pdb=" O MET A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 719 removed outlier: 4.136A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.766A pdb=" N LEU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.056A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.791A pdb=" N ALA B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.481A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 416 through 425 Processing helix chain 'B' and resid 455 through 472 removed outlier: 3.515A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 607 through 610 No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.751A pdb=" N GLU B 685 " --> pdb=" O MET B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 713 through 730 Processing helix chain 'B' and resid 736 through 748 removed outlier: 3.729A pdb=" N GLU B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.690A pdb=" N THR C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.308A pdb=" N LYS C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 113 through 128 removed outlier: 3.687A pdb=" N GLU C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 228 through 231 No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 254 through 274 removed outlier: 4.846A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 543 through 556 Processing helix chain 'C' and resid 558 through 567 Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.638A pdb=" N ALA C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.569A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 Processing helix chain 'C' and resid 690 through 693 Processing helix chain 'C' and resid 714 through 718 Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.557A pdb=" N GLU A 144 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY A 122 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET A 146 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR A 124 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 148 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 291 through 293 removed outlier: 6.128A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 498 through 502 removed outlier: 3.679A pdb=" N GLY A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A 540 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 324 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 615 through 620 removed outlier: 7.050A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= H, first strand: chain 'B' and resid 178 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.671A pdb=" N ILE B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 226 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 482 through 485 Processing sheet with id= K, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 488 through 491 Processing sheet with id= M, first strand: chain 'C' and resid 135 through 137 Processing sheet with id= N, first strand: chain 'C' and resid 143 through 148 Processing sheet with id= O, first strand: chain 'C' and resid 289 through 291 Processing sheet with id= P, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.716A pdb=" N LEU C 330 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C 337 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU C 362 " --> pdb=" O GLY C 337 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= R, first strand: chain 'C' and resid 453 through 455 Processing sheet with id= S, first strand: chain 'C' and resid 639 through 641 Processing sheet with id= T, first strand: chain 'C' and resid 660 through 662 Processing sheet with id= U, first strand: chain 'C' and resid 725 through 729 667 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4961 1.33 - 1.45: 3317 1.45 - 1.57: 10112 1.57 - 1.69: 78 1.69 - 1.81: 224 Bond restraints: 18692 Sorted by residual: bond pdb=" C2E GTG M 1 " pdb=" C3E GTG M 1 " ideal model delta sigma weight residual 1.254 1.501 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C3D GTG M 1 " pdb=" C4D GTG M 1 " ideal model delta sigma weight residual 1.298 1.534 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.538 1.321 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C5A GTG M 1 " pdb=" C6A GTG M 1 " ideal model delta sigma weight residual 1.539 1.339 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4E GTG M 1 " pdb=" O4E GTG M 1 " ideal model delta sigma weight residual 1.294 1.460 -0.166 2.00e-02 2.50e+03 6.85e+01 ... (remaining 18687 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.17: 446 104.17 - 112.06: 8956 112.06 - 119.96: 7731 119.96 - 127.85: 8032 127.85 - 135.75: 205 Bond angle restraints: 25370 Sorted by residual: angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C4A GTG M 1 " ideal model delta sigma weight residual 93.21 130.33 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C8A GTG M 1 " ideal model delta sigma weight residual 157.61 120.83 36.78 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C8B GTG M 1 " ideal model delta sigma weight residual 99.21 122.56 -23.35 3.00e+00 1.11e-01 6.06e+01 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C4B GTG M 1 " ideal model delta sigma weight residual 152.69 130.00 22.69 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C LEU B 163 " pdb=" N ILE B 164 " pdb=" CA ILE B 164 " ideal model delta sigma weight residual 120.24 123.92 -3.68 6.30e-01 2.52e+00 3.41e+01 ... (remaining 25365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.00: 10268 19.00 - 38.00: 857 38.00 - 57.01: 227 57.01 - 76.01: 64 76.01 - 95.01: 15 Dihedral angle restraints: 11431 sinusoidal: 5114 harmonic: 6317 Sorted by residual: dihedral pdb=" CA GLN B 441 " pdb=" C GLN B 441 " pdb=" N SER B 442 " pdb=" CA SER B 442 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLU A 29 " pdb=" C GLU A 29 " pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLN C 607 " pdb=" C GLN C 607 " pdb=" N GLU C 608 " pdb=" CA GLU C 608 " ideal model delta harmonic sigma weight residual 180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2598 0.085 - 0.170: 208 0.170 - 0.255: 8 0.255 - 0.340: 0 0.340 - 0.425: 2 Chirality restraints: 2816 Sorted by residual: chirality pdb=" C3D GTG M 1 " pdb=" C2D GTG M 1 " pdb=" C4D GTG M 1 " pdb=" O3D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.38 -2.80 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C3E GTG M 1 " pdb=" C2E GTG M 1 " pdb=" C4E GTG M 1 " pdb=" O3E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.43 -2.81 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2813 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.041 2.00e-02 2.50e+03 1.96e-02 1.06e+01 pdb=" N9 A V 4 " 0.048 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 656 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO C 657 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 657 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 657 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 393 " -0.040 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B 394 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " -0.034 5.00e-02 4.00e+02 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 249 2.64 - 3.20: 14806 3.20 - 3.77: 28184 3.77 - 4.33: 40464 4.33 - 4.90: 66229 Nonbonded interactions: 149932 Sorted by model distance: nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP A 109 " pdb="MG MG A 801 " model vdw 2.109 2.170 nonbonded pdb=" OE2 GLU A 81 " pdb="MG MG A 801 " model vdw 2.141 2.170 nonbonded pdb=" OD2 ASP B 445 " pdb="MG MG B 801 " model vdw 2.154 2.170 nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.261 2.440 ... (remaining 149927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.080 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 52.850 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 18692 Z= 0.541 Angle : 0.850 37.123 25370 Z= 0.429 Chirality : 0.049 0.425 2816 Planarity : 0.007 0.064 3112 Dihedral : 15.710 95.009 7361 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.87 % Allowed : 8.07 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.13), residues: 2176 helix: -2.48 (0.12), residues: 948 sheet: -2.07 (0.31), residues: 231 loop : -2.78 (0.15), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 437 HIS 0.007 0.001 HIS A 41 PHE 0.016 0.002 PHE B 199 TYR 0.019 0.002 TYR C 207 ARG 0.005 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 250 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 85 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6803 (ttm-80) REVERT: A 165 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: C 208 MET cc_start: 0.7860 (ptm) cc_final: 0.7640 (ptt) REVERT: C 233 MET cc_start: 0.8845 (tpp) cc_final: 0.8449 (tpp) REVERT: C 584 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8446 (pp) outliers start: 112 outliers final: 35 residues processed: 345 average time/residue: 0.3526 time to fit residues: 174.2044 Evaluate side-chains 184 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 19 ASN A 52 ASN A 92 GLN A 222 ASN A 357 GLN ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 610 ASN A 693 ASN B 47 HIS B 265 ASN B 310 ASN B 314 ASN B 346 ASN B 475 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN B 675 ASN B 680 ASN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 354 GLN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN C 442 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 727 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18692 Z= 0.188 Angle : 0.513 6.786 25370 Z= 0.269 Chirality : 0.039 0.226 2816 Planarity : 0.004 0.043 3112 Dihedral : 11.824 95.323 2999 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.14 % Allowed : 12.31 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2176 helix: -0.67 (0.15), residues: 971 sheet: -1.62 (0.32), residues: 240 loop : -2.30 (0.17), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 PHE 0.010 0.001 PHE A 629 TYR 0.014 0.001 TYR A 154 ARG 0.006 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 152 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.8748 (p) cc_final: 0.8455 (t) REVERT: A 165 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: C 208 MET cc_start: 0.8056 (ptm) cc_final: 0.7848 (ptt) REVERT: C 469 MET cc_start: 0.6779 (mmm) cc_final: 0.6573 (mmm) REVERT: C 584 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8421 (pp) outliers start: 60 outliers final: 34 residues processed: 201 average time/residue: 0.3023 time to fit residues: 92.7841 Evaluate side-chains 177 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 531 ASN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18692 Z= 0.160 Angle : 0.476 9.120 25370 Z= 0.245 Chirality : 0.038 0.216 2816 Planarity : 0.004 0.041 3112 Dihedral : 11.380 94.859 2973 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.83 % Allowed : 12.99 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2176 helix: 0.27 (0.17), residues: 971 sheet: -1.33 (0.31), residues: 260 loop : -1.91 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.009 0.001 PHE A 629 TYR 0.014 0.001 TYR A 154 ARG 0.005 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 147 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.8774 (p) cc_final: 0.8459 (t) REVERT: A 165 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 352 MET cc_start: 0.6826 (mmm) cc_final: 0.6575 (tpt) REVERT: A 544 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 208 MET cc_start: 0.8038 (ptm) cc_final: 0.7831 (ptt) outliers start: 54 outliers final: 33 residues processed: 191 average time/residue: 0.2969 time to fit residues: 87.7543 Evaluate side-chains 171 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 560 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18692 Z= 0.139 Angle : 0.461 7.992 25370 Z= 0.235 Chirality : 0.038 0.204 2816 Planarity : 0.003 0.038 3112 Dihedral : 11.108 93.773 2963 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.57 % Allowed : 13.93 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2176 helix: 0.73 (0.17), residues: 974 sheet: -1.18 (0.32), residues: 249 loop : -1.70 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.009 0.001 PHE A 132 TYR 0.027 0.001 TYR A 154 ARG 0.004 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 2.092 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 3 THR cc_start: 0.8735 (p) cc_final: 0.8420 (t) REVERT: A 544 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8771 (tp) REVERT: C 404 MET cc_start: 0.8302 (mmm) cc_final: 0.8008 (tpp) REVERT: C 584 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8394 (pp) outliers start: 49 outliers final: 33 residues processed: 178 average time/residue: 0.2988 time to fit residues: 82.4583 Evaluate side-chains 168 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN B 247 GLN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 HIS ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN C 552 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 692 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 18692 Z= 0.359 Angle : 0.562 6.617 25370 Z= 0.290 Chirality : 0.042 0.183 2816 Planarity : 0.004 0.041 3112 Dihedral : 11.108 100.005 2955 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.04 % Allowed : 13.83 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2176 helix: 0.67 (0.17), residues: 981 sheet: -1.20 (0.31), residues: 260 loop : -1.63 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 437 HIS 0.004 0.001 HIS A 41 PHE 0.016 0.002 PHE A 132 TYR 0.020 0.002 TYR C 207 ARG 0.004 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 404 MET cc_start: 0.8079 (mmm) cc_final: 0.7809 (tpp) REVERT: C 423 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (mp) REVERT: C 584 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8429 (pp) outliers start: 58 outliers final: 46 residues processed: 185 average time/residue: 0.2902 time to fit residues: 83.0338 Evaluate side-chains 179 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18692 Z= 0.130 Angle : 0.462 6.638 25370 Z= 0.238 Chirality : 0.038 0.177 2816 Planarity : 0.003 0.035 3112 Dihedral : 10.977 97.587 2955 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.36 % Allowed : 14.77 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2176 helix: 1.08 (0.17), residues: 976 sheet: -1.09 (0.32), residues: 259 loop : -1.46 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 437 HIS 0.004 0.000 HIS C 366 PHE 0.008 0.001 PHE B 739 TYR 0.030 0.001 TYR A 154 ARG 0.003 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 412 MET cc_start: 0.7119 (tmm) cc_final: 0.6899 (tmm) REVERT: C 584 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8370 (pp) outliers start: 45 outliers final: 33 residues processed: 174 average time/residue: 0.3203 time to fit residues: 85.1611 Evaluate side-chains 166 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 132 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18692 Z= 0.172 Angle : 0.468 7.292 25370 Z= 0.239 Chirality : 0.038 0.169 2816 Planarity : 0.003 0.034 3112 Dihedral : 10.942 97.254 2955 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.78 % Allowed : 14.41 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2176 helix: 1.21 (0.17), residues: 977 sheet: -1.05 (0.32), residues: 259 loop : -1.35 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.010 0.001 PHE A 132 TYR 0.025 0.001 TYR A 154 ARG 0.003 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 562 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7455 (ttp80) REVERT: C 423 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8497 (mp) REVERT: C 584 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8395 (pp) outliers start: 53 outliers final: 42 residues processed: 176 average time/residue: 0.3048 time to fit residues: 82.9014 Evaluate side-chains 176 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18692 Z= 0.124 Angle : 0.452 8.676 25370 Z= 0.229 Chirality : 0.037 0.159 2816 Planarity : 0.003 0.063 3112 Dihedral : 10.806 94.940 2952 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 15.35 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2176 helix: 1.41 (0.17), residues: 970 sheet: -0.92 (0.32), residues: 259 loop : -1.25 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.003 0.000 HIS C 366 PHE 0.011 0.001 PHE A 709 TYR 0.020 0.001 TYR A 154 ARG 0.017 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 562 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7416 (ttp80) REVERT: C 584 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8412 (pp) outliers start: 43 outliers final: 36 residues processed: 172 average time/residue: 0.3219 time to fit residues: 84.1659 Evaluate side-chains 164 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18692 Z= 0.179 Angle : 0.476 9.254 25370 Z= 0.240 Chirality : 0.039 0.172 2816 Planarity : 0.003 0.057 3112 Dihedral : 10.769 95.747 2949 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.36 % Allowed : 15.40 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2176 helix: 1.36 (0.17), residues: 979 sheet: -0.89 (0.32), residues: 259 loop : -1.19 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 PHE 0.011 0.001 PHE C 565 TYR 0.020 0.001 TYR A 154 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8554 (mm) REVERT: C 423 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 584 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8388 (pp) outliers start: 45 outliers final: 35 residues processed: 166 average time/residue: 0.3048 time to fit residues: 77.8029 Evaluate side-chains 164 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18692 Z= 0.216 Angle : 0.495 9.664 25370 Z= 0.250 Chirality : 0.039 0.149 2816 Planarity : 0.003 0.053 3112 Dihedral : 10.811 97.921 2949 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.25 % Allowed : 15.40 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2176 helix: 1.28 (0.17), residues: 989 sheet: -0.90 (0.32), residues: 259 loop : -1.20 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.003 0.001 HIS A 41 PHE 0.010 0.001 PHE B 7 TYR 0.022 0.001 TYR A 154 ARG 0.014 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 562 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7479 (ttp80) REVERT: C 423 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 441 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8430 (tm) REVERT: C 584 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8400 (pp) outliers start: 43 outliers final: 35 residues processed: 164 average time/residue: 0.3047 time to fit residues: 76.5776 Evaluate side-chains 166 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 527 GLN Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 179 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.054763 restraints weight = 52518.565| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.36 r_work: 0.2897 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18692 Z= 0.176 Angle : 0.480 8.755 25370 Z= 0.244 Chirality : 0.039 0.150 2816 Planarity : 0.003 0.064 3112 Dihedral : 10.788 97.738 2948 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.36 % Allowed : 15.51 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2176 helix: 1.36 (0.17), residues: 982 sheet: -0.85 (0.32), residues: 259 loop : -1.17 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 PHE 0.010 0.001 PHE C 565 TYR 0.021 0.001 TYR A 154 ARG 0.014 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.65 seconds wall clock time: 64 minutes 21.56 seconds (3861.56 seconds total)