Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 7 22:45:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_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_4512/05_2023/6qct_4512_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qct_4512/05_2023/6qct_4512_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 10.09, per 1000 atoms: 0.55 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: 7.33 Conformation dependent library (CDL) restraints added in 2.7 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: 6.52 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: 6.32 Time building geometry restraints manager: 7.82 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: 10229 19.00 - 38.00: 831 38.00 - 57.01: 204 57.01 - 76.01: 30 76.01 - 95.01: 14 Dihedral angle restraints: 11308 sinusoidal: 4991 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 11305 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.830 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 52.480 Find NCS groups from input model: 0.720 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.450 ------------------------------------------------------------------------------- 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 : 14.843 95.009 7238 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 % 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 *********************** 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 : 2.250 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 outliers start: 112 outliers final: 35 residues processed: 345 average time/residue: 0.3727 time to fit residues: 183.5816 Evaluate side-chains 180 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1684 time to fit residues: 14.4046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 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: 7.9990 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: 1.2784 ------------------------------------------------------------------------------- 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 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 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: 0.8163 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 18692 Z= 0.170 Angle : 0.506 6.795 25370 Z= 0.265 Chirality : 0.039 0.221 2816 Planarity : 0.004 0.042 3112 Dihedral : 7.343 94.684 2814 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.99 % 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: -2.21 (0.16), residues: 2176 helix: -0.62 (0.15), residues: 969 sheet: -1.60 (0.32), residues: 238 loop : -2.29 (0.17), residues: 969 *********************** 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 192 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 2.301 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 outliers start: 38 outliers final: 17 residues processed: 182 average time/residue: 0.3371 time to fit residues: 92.6631 Evaluate side-chains 160 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 2.464 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1800 time to fit residues: 9.0428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.4444 > 50: distance: 48 - 209: 23.104 distance: 51 - 206: 14.891 distance: 112 - 135: 7.115 distance: 116 - 144: 7.074 distance: 125 - 155: 3.523 distance: 130 - 135: 5.989 distance: 131 - 164: 6.269 distance: 135 - 136: 5.438 distance: 136 - 139: 6.585 distance: 137 - 138: 6.499 distance: 137 - 144: 7.716 distance: 139 - 140: 7.133 distance: 140 - 141: 9.868 distance: 141 - 142: 7.209 distance: 141 - 143: 6.687 distance: 144 - 145: 5.362 distance: 145 - 146: 4.860 distance: 145 - 148: 5.358 distance: 146 - 147: 6.784 distance: 146 - 155: 5.223 distance: 148 - 149: 9.256 distance: 149 - 150: 3.933 distance: 150 - 151: 3.767 distance: 155 - 156: 4.928 distance: 156 - 159: 6.111 distance: 157 - 158: 5.204 distance: 157 - 164: 3.539 distance: 159 - 160: 3.346 distance: 160 - 161: 5.292 distance: 161 - 162: 6.126 distance: 161 - 163: 8.999 distance: 165 - 166: 6.141 distance: 165 - 168: 13.349 distance: 166 - 167: 12.716 distance: 166 - 172: 3.488 distance: 168 - 169: 13.487 distance: 169 - 170: 11.978 distance: 169 - 171: 7.073 distance: 172 - 173: 5.002 distance: 173 - 174: 13.888 distance: 173 - 176: 10.731 distance: 174 - 175: 16.268 distance: 174 - 179: 21.101 distance: 176 - 177: 12.041 distance: 179 - 180: 4.731 distance: 180 - 181: 15.445 distance: 180 - 183: 21.137 distance: 181 - 182: 10.089 distance: 184 - 185: 7.298 distance: 185 - 186: 7.011 distance: 185 - 188: 8.956 distance: 186 - 187: 41.547 distance: 186 - 195: 23.373 distance: 188 - 189: 5.846 distance: 191 - 192: 4.078 distance: 192 - 193: 3.655 distance: 192 - 194: 3.662 distance: 195 - 196: 28.645 distance: 196 - 197: 11.821 distance: 196 - 199: 27.997 distance: 197 - 206: 20.022 distance: 199 - 200: 26.950 distance: 200 - 201: 20.181 distance: 201 - 202: 12.182 distance: 202 - 203: 6.032 distance: 203 - 205: 6.231 distance: 206 - 207: 10.716 distance: 207 - 208: 12.720 distance: 207 - 210: 18.180 distance: 208 - 209: 15.692 distance: 208 - 217: 8.483 distance: 210 - 211: 4.633 distance: 211 - 212: 16.042 distance: 212 - 213: 3.056 distance: 213 - 214: 9.034 distance: 214 - 215: 7.060 distance: 214 - 216: 11.016 distance: 217 - 218: 8.701 distance: 218 - 219: 4.698 distance: 218 - 221: 17.062 distance: 219 - 220: 19.284 distance: 221 - 222: 4.637 distance: 222 - 223: 15.223 distance: 222 - 224: 10.665 distance: 223 - 225: 20.090 distance: 224 - 226: 20.418 distance: 225 - 227: 16.637 distance: 226 - 227: 24.946