Starting phenix.real_space_refine on Fri Jun 20 00:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.map" model { file = "/net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edg_28034/06_2025/8edg_28034.cif" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 Zn 6 6.06 5 P 212 5.49 5 S 112 5.16 5 C 14194 2.51 5 N 4050 2.21 5 O 4784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23358 Number of models: 1 Model: "" Number of chains: 18 Chain: "M" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 6} Chain: "N" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "O" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1126 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "R" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1126 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "P" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "C" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "I" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 601 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "G" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "K" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 601 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4813 SG CYS A 51 106.456 85.404 40.489 1.00140.54 S ATOM 4839 SG CYS A 54 108.768 82.042 40.981 1.00149.72 S ATOM 4998 SG CYS A 73 107.446 84.117 43.987 1.00166.29 S ATOM 9245 SG CYS C 51 62.941 86.411 103.549 1.00176.12 S ATOM 9271 SG CYS C 54 65.615 85.962 106.173 1.00183.89 S ATOM 9430 SG CYS C 73 65.825 84.041 102.802 1.00186.21 S ATOM 13677 SG CYS I 51 88.952 61.126 53.931 1.00157.62 S ATOM 13703 SG CYS I 54 86.782 62.521 51.131 1.00166.93 S ATOM 13862 SG CYS I 73 87.778 64.809 54.062 1.00176.76 S ATOM 14278 SG CYS E 51 117.194 40.229 67.933 1.00162.32 S ATOM 14304 SG CYS E 54 116.798 40.517 64.180 1.00169.46 S ATOM 14463 SG CYS E 73 114.497 42.536 66.354 1.00153.25 S ATOM 18710 SG CYS G 51 116.746 101.585 112.993 1.00147.53 S ATOM 18736 SG CYS G 54 113.369 102.965 114.274 1.00158.46 S ATOM 18895 SG CYS G 73 113.488 100.760 111.150 1.00123.95 S ATOM 23142 SG CYS K 51 98.448 75.983 118.061 1.00176.17 S ATOM 23168 SG CYS K 54 101.615 73.919 117.493 1.00165.17 S ATOM 23327 SG CYS K 73 100.708 76.601 114.957 1.00156.70 S Time building chain proxies: 13.04, per 1000 atoms: 0.56 Number of scatterers: 23358 At special positions: 0 Unit cell: (200.68, 160.08, 155.44, 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) Zn 6 29.99 S 112 16.00 P 212 15.00 O 4784 8.00 N 4050 7.00 C 14194 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 54 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 71 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 51 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 54 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 71 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 54 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 73 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 51 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" NE2 HIS G 71 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 54 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 51 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 71 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 54 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 51 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 73 " pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" NE2 HIS K 71 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 51 " Number of angles added : 18 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 16 sheets defined 61.7% alpha, 6.8% beta 49 base pairs and 142 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.396A pdb=" N GLU A 8 " --> pdb=" O MET A 4 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.557A pdb=" N HIS A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.669A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.736A pdb=" N ASP A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.677A pdb=" N VAL A 112 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 143 through 172 removed outlier: 4.203A pdb=" N ARG A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 281 through 301 Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.407A pdb=" N HIS A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 320 through 344 removed outlier: 4.425A pdb=" N THR A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 4.145A pdb=" N ILE A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.729A pdb=" N ILE A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 435 removed outlier: 4.034A pdb=" N TYR A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.766A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 539 through 551 removed outlier: 4.203A pdb=" N LYS A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.579A pdb=" N LYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 583 through 587 removed outlier: 4.131A pdb=" N ASN A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.929A pdb=" N TRP C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 75 removed outlier: 6.294A pdb=" N LYS C 72 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N CYS C 73 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 106 removed outlier: 3.542A pdb=" N LYS C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 114 through 132 Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.987A pdb=" N LEU C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 141' Processing helix chain 'C' and resid 143 through 171 removed outlier: 4.350A pdb=" N ARG C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 3.739A pdb=" N PHE C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 281 through 302 Proline residue: C 287 - end of helix Processing helix chain 'C' and resid 321 through 344 removed outlier: 5.629A pdb=" N GLU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 353 through 375 Processing helix chain 'C' and resid 385 through 396 removed outlier: 3.800A pdb=" N CYS C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 426 through 435 removed outlier: 4.198A pdb=" N TYR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.791A pdb=" N GLU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 539 through 547 Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.870A pdb=" N LEU C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 removed outlier: 4.135A pdb=" N GLU C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.523A pdb=" N VAL C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.916A pdb=" N LEU I 77 " --> pdb=" O CYS I 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.877A pdb=" N ARG E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.884A pdb=" N SER E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU E 77 " --> pdb=" O CYS E 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 78 " --> pdb=" O CYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 105 removed outlier: 3.633A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.637A pdb=" N VAL E 112 " --> pdb=" O PHE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 132 Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.871A pdb=" N LEU E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 172 removed outlier: 4.506A pdb=" N ARG E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 234 Processing helix chain 'E' and resid 250 through 257 Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 281 through 301 Proline residue: E 287 - end of helix removed outlier: 3.934A pdb=" N ALA E 301 " --> pdb=" O TYR E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 345 through 352 removed outlier: 3.587A pdb=" N ILE E 349 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 350 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS E 351 " --> pdb=" O ARG E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 375 Processing helix chain 'E' and resid 385 through 396 Processing helix chain 'E' and resid 403 through 421 Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 426 through 435 removed outlier: 3.786A pdb=" N TYR E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE E 435 " --> pdb=" O THR E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 3.790A pdb=" N ALA E 448 " --> pdb=" O GLN E 444 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 530 Processing helix chain 'E' and resid 539 through 548 Processing helix chain 'E' and resid 553 through 563 removed outlier: 3.737A pdb=" N LEU E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 582 removed outlier: 4.037A pdb=" N GLU E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 607 Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.572A pdb=" N VAL G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.546A pdb=" N CYS G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 70' Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 87 through 106 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.620A pdb=" N VAL G 112 " --> pdb=" O PHE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 removed outlier: 3.790A pdb=" N ASP G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.607A pdb=" N LEU G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 141 " --> pdb=" O VAL G 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 136 through 141' Processing helix chain 'G' and resid 143 through 172 removed outlier: 4.395A pdb=" N ARG G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 235 Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 281 through 301 Proline residue: G 287 - end of helix Processing helix chain 'G' and resid 320 through 332 removed outlier: 4.174A pdb=" N THR G 324 " --> pdb=" O ASN G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 removed outlier: 4.285A pdb=" N GLU G 342 " --> pdb=" O GLN G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 removed outlier: 4.041A pdb=" N ILE G 349 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 350 " --> pdb=" O THR G 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 345 through 350' Processing helix chain 'G' and resid 353 through 375 removed outlier: 4.080A pdb=" N ILE G 357 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 396 Processing helix chain 'G' and resid 403 through 421 Processing helix chain 'G' and resid 426 through 435 removed outlier: 4.012A pdb=" N TYR G 430 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE G 435 " --> pdb=" O THR G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 460 removed outlier: 3.818A pdb=" N GLN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 453 " --> pdb=" O GLN G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 529 removed outlier: 3.782A pdb=" N LYS G 529 " --> pdb=" O GLU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 548 Processing helix chain 'G' and resid 551 through 563 Processing helix chain 'G' and resid 568 through 582 Processing helix chain 'G' and resid 590 through 607 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 28 through 33 removed outlier: 3.589A pdb=" N VAL K 33 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.815A pdb=" N LEU K 77 " --> pdb=" O CYS K 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 12.239A pdb=" N ALA A 35 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLY A 47 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE A 37 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 213 removed outlier: 5.799A pdb=" N ASP A 206 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR A 198 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 208 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 196 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 210 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 194 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 180 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 195 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 177 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.649A pdb=" N THR C 21 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 36 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 37 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TRP C 48 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 205 through 213 removed outlier: 3.518A pdb=" N ARG C 205 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 198 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 207 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 194 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU C 211 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 192 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C 213 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN C 190 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 180 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 195 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR C 178 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 177 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 245 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'I' and resid 48 through 50 removed outlier: 3.676A pdb=" N VAL I 49 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU I 58 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.934A pdb=" N LYS E 19 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 38 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 183 removed outlier: 7.893A pdb=" N ASN E 190 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N SER E 213 " --> pdb=" O ASN E 190 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 192 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU E 211 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL E 194 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR E 198 " --> pdb=" O ARG E 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 245 through 246 removed outlier: 6.148A pdb=" N PHE E 245 " --> pdb=" O ILE E 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.563A pdb=" N THR G 21 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP G 36 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 11.866A pdb=" N ALA G 35 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLY G 47 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE G 37 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 176 through 177 removed outlier: 3.642A pdb=" N VAL G 246 " --> pdb=" O ALA G 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 179 through 183 removed outlier: 4.376A pdb=" N ASP G 180 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY G 193 " --> pdb=" O ASP G 180 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP G 182 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 197 through 199 Processing sheet with id=AB6, first strand: chain 'K' and resid 20 through 21 removed outlier: 3.579A pdb=" N ASP K 36 " --> pdb=" O THR K 21 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 48 through 50 978 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 142 stacking parallelities Total time for adding SS restraints: 8.15 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6282 1.34 - 1.46: 5092 1.46 - 1.58: 12302 1.58 - 1.70: 422 1.70 - 1.82: 146 Bond restraints: 24244 Sorted by residual: bond pdb=" CG1 ILE E 166 " pdb=" CD1 ILE E 166 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.55e+00 bond pdb=" C3' DG R 9 " pdb=" O3' DG R 9 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" C3' DA R 52 " pdb=" O3' DA R 52 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CA VAL C 386 " pdb=" CB VAL C 386 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.39e+00 ... (remaining 24239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 32959 1.92 - 3.85: 608 3.85 - 5.77: 57 5.77 - 7.69: 13 7.69 - 9.62: 3 Bond angle restraints: 33640 Sorted by residual: angle pdb=" C ILE A 419 " pdb=" N ILE A 420 " pdb=" CA ILE A 420 " ideal model delta sigma weight residual 123.16 118.31 4.85 1.06e+00 8.90e-01 2.10e+01 angle pdb=" C SER E 341 " pdb=" N GLU E 342 " pdb=" CA GLU E 342 " ideal model delta sigma weight residual 122.38 115.01 7.37 1.81e+00 3.05e-01 1.66e+01 angle pdb=" C VAL A 417 " pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 122.38 115.33 7.05 1.81e+00 3.05e-01 1.52e+01 angle pdb=" CA GLU E 203 " pdb=" CB GLU E 203 " pdb=" CG GLU E 203 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" N VAL E 400 " pdb=" CA VAL E 400 " pdb=" C VAL E 400 " ideal model delta sigma weight residual 113.39 109.06 4.33 1.47e+00 4.63e-01 8.67e+00 ... (remaining 33635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 13056 34.63 - 69.25: 1108 69.25 - 103.88: 41 103.88 - 138.50: 3 138.50 - 173.13: 4 Dihedral angle restraints: 14212 sinusoidal: 7262 harmonic: 6950 Sorted by residual: dihedral pdb=" C4' DG R 9 " pdb=" C3' DG R 9 " pdb=" O3' DG R 9 " pdb=" P DC R 10 " ideal model delta sinusoidal sigma weight residual 220.00 46.87 173.13 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA Q 15 " pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " pdb=" P DG Q 16 " ideal model delta sinusoidal sigma weight residual 220.00 54.14 165.86 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA R 52 " pdb=" C3' DA R 52 " pdb=" O3' DA R 52 " pdb=" P DC R 53 " ideal model delta sinusoidal sigma weight residual 220.00 74.87 145.13 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 14209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3030 0.045 - 0.089: 649 0.089 - 0.134: 130 0.134 - 0.179: 8 0.179 - 0.224: 1 Chirality restraints: 3818 Sorted by residual: chirality pdb=" CA MET E 286 " pdb=" N MET E 286 " pdb=" C MET E 286 " pdb=" CB MET E 286 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU G 557 " pdb=" CB LEU G 557 " pdb=" CD1 LEU G 557 " pdb=" CD2 LEU G 557 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA GLU C 394 " pdb=" N GLU C 394 " pdb=" C GLU C 394 " pdb=" CB GLU C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 3815 not shown) Planarity restraints: 3470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 564 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 565 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 544 " -0.013 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP E 544 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP E 544 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 544 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 544 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 544 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 544 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 544 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 544 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 544 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 437 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO G 438 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 438 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 438 " 0.028 5.00e-02 4.00e+02 ... (remaining 3467 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 779 2.69 - 3.25: 23513 3.25 - 3.80: 39763 3.80 - 4.35: 49243 4.35 - 4.90: 74426 Nonbonded interactions: 187724 Sorted by model distance: nonbonded pdb=" O SER G 76 " pdb=" OG SER G 80 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 87 " pdb=" OD1 ASP A 89 " model vdw 2.177 3.040 nonbonded pdb=" O ASP G 173 " pdb=" NZ LYS G 244 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR E 604 " pdb=" OE1 GLN G 100 " model vdw 2.217 3.040 nonbonded pdb=" OP1 DA Q 29 " pdb=" NZ LYS C 72 " model vdw 2.218 3.120 ... (remaining 187719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'N' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'R' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 59.900 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.003 0.062 24268 Z= 0.138 Angle : 0.611 11.018 33658 Z= 0.345 Chirality : 0.038 0.224 3818 Planarity : 0.004 0.062 3470 Dihedral : 21.429 173.128 9656 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2328 helix: 0.86 (0.15), residues: 1276 sheet: -1.76 (0.33), residues: 210 loop : -1.45 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 544 HIS 0.006 0.001 HIS E 134 PHE 0.028 0.001 PHE C 524 TYR 0.020 0.001 TYR G 225 ARG 0.007 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.17540 ( 1093) hydrogen bonds : angle 6.66273 ( 3022) metal coordination : bond 0.00966 ( 24) metal coordination : angle 3.09846 ( 18) covalent geometry : bond 0.00279 (24244) covalent geometry : angle 0.60711 (33640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 202 ASN cc_start: 0.7754 (m110) cc_final: 0.7545 (m-40) REVERT: A 211 LEU cc_start: 0.8910 (tp) cc_final: 0.8611 (tp) REVERT: A 361 VAL cc_start: 0.8897 (t) cc_final: 0.8670 (t) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1339 time to fit residues: 12.9873 Evaluate side-chains 43 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.474 Evaluate side-chains 20 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.066 Fit side-chains REVERT: I 8 GLU cc_start: 0.7050 (tp30) cc_final: 0.5761 (tt0) REVERT: I 17 LEU cc_start: 0.6393 (mt) cc_final: 0.5558 (mp) REVERT: I 32 ASN cc_start: 0.6636 (p0) cc_final: 0.6028 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1063 time to fit residues: 2.3447 Evaluate side-chains 10 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.065 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0068 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0341 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0402 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 120 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 229 optimal weight: 0.0470 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 302 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077761 restraints weight = 20063.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079169 restraints weight = 14037.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080148 restraints weight = 10895.225| |-----------------------------------------------------------------------------| r_work (final): 0.3365 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.122676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112962 restraints weight = 2733.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112959 restraints weight = 2637.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112957 restraints weight = 2640.214| |-----------------------------------------------------------------------------| r_work (final): 0.3999 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.101530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097644 restraints weight = 815.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.098696 restraints weight = 433.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099580 restraints weight = 223.562| |-----------------------------------------------------------------------------| r_work (final): 0.3771 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057901 restraints weight = 9269.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059074 restraints weight = 3769.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059758 restraints weight = 2259.992| |-----------------------------------------------------------------------------| r_work (final): 0.3024 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068974 restraints weight = 9978.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068831 restraints weight = 7663.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069389 restraints weight = 5767.674| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 1.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24268 Z= 0.217 Angle : 0.819 17.278 33658 Z= 0.456 Chirality : 0.045 0.274 3818 Planarity : 0.005 0.058 3470 Dihedral : 24.930 142.117 4884 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.81 % Favored : 94.50 % Rotamer: Outliers : 1.67 % Allowed : 5.76 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2328 helix: 0.55 (0.14), residues: 1390 sheet: -0.83 (0.31), residues: 240 loop : -1.57 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 421 HIS 0.006 0.001 HIS E 134 PHE 0.029 0.002 PHE G 124 TYR 0.009 0.001 TYR A 436 ARG 0.006 0.001 ARG G 70 Details of bonding type rmsd hydrogen bonds : bond 0.12178 ( 1093) hydrogen bonds : angle 5.30102 ( 3022) metal coordination : bond 0.03295 ( 24) metal coordination : angle 11.52899 ( 18) covalent geometry : bond 0.00448 (24244) covalent geometry : angle 0.77500 (33640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8676 (tt0) cc_final: 0.8361 (tp30) REVERT: A 360 MET cc_start: 0.8684 (mtm) cc_final: 0.8321 (mtm) REVERT: A 392 VAL cc_start: 0.8408 (t) cc_final: 0.8203 (p) REVERT: A 422 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7990 (pp20) REVERT: A 425 LEU cc_start: 0.8615 (mt) cc_final: 0.8140 (mt) outliers start: 9 outliers final: 1 residues processed: 78 average time/residue: 0.1717 time to fit residues: 17.3723 Evaluate side-chains 42 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.519 Evaluate side-chains 30 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.075 Fit side-chains REVERT: K 34 LEU cc_start: 0.7563 (tp) cc_final: 0.7128 (tp) REVERT: K 77 LEU cc_start: 0.6183 (mm) cc_final: 0.5977 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2087 time to fit residues: 6.5392 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.075 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0078 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0786 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0470 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 103 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 193 optimal weight: 4.9990 chunk 222 optimal weight: 0.0060 chunk 134 optimal weight: 0.0470 chunk 140 optimal weight: 0.0170 chunk 146 optimal weight: 0.4980 overall best weight: 0.1532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 14 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077064 restraints weight = 20723.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078629 restraints weight = 14155.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079678 restraints weight = 10627.335| |-----------------------------------------------------------------------------| r_work (final): 0.3364 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.126303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.111695 restraints weight = 3239.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.113115 restraints weight = 2454.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.113901 restraints weight = 2029.354| |-----------------------------------------------------------------------------| r_work (final): 0.3978 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.103254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.099477 restraints weight = 792.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100620 restraints weight = 343.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101457 restraints weight = 193.095| |-----------------------------------------------------------------------------| r_work (final): 0.3728 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058165 restraints weight = 9637.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059316 restraints weight = 3922.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.060005 restraints weight = 2375.833| |-----------------------------------------------------------------------------| r_work (final): 0.3038 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.070140 restraints weight = 9893.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069761 restraints weight = 5826.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070103 restraints weight = 5150.558| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 1.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 24268 Z= 0.336 Angle : 1.095 42.950 33658 Z= 0.582 Chirality : 0.055 0.406 3818 Planarity : 0.009 0.164 3470 Dihedral : 25.024 142.832 4884 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.24 % Rotamer: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2328 helix: 0.07 (0.14), residues: 1374 sheet: -0.76 (0.31), residues: 240 loop : -1.67 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 319 HIS 0.003 0.001 HIS I 71 PHE 0.022 0.002 PHE A 124 TYR 0.022 0.001 TYR C 604 ARG 0.041 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.11995 ( 1093) hydrogen bonds : angle 5.48658 ( 3022) metal coordination : bond 0.03271 ( 24) metal coordination : angle 11.35731 ( 18) covalent geometry : bond 0.00744 (24244) covalent geometry : angle 1.06352 (33640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8609 (tt0) cc_final: 0.8315 (tp30) REVERT: A 360 MET cc_start: 0.8687 (mtm) cc_final: 0.8237 (mtm) REVERT: A 418 ARG cc_start: 0.7957 (pmt-80) cc_final: 0.7749 (ptm160) REVERT: A 422 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7943 (pp20) REVERT: A 425 LEU cc_start: 0.8659 (mt) cc_final: 0.8375 (mt) REVERT: A 442 MET cc_start: 0.7432 (pmm) cc_final: 0.6129 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1817 time to fit residues: 16.7598 Evaluate side-chains 43 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.521 Evaluate side-chains 19 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.076 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.1792 time to fit residues: 3.4451 Evaluate side-chains 13 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.075 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0075 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0395 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0445 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 33 optimal weight: 0.2980 chunk 134 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 212 optimal weight: 0.0000 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 234 optimal weight: 0.3980 chunk 206 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.077100 restraints weight = 21721.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078594 restraints weight = 15350.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079628 restraints weight = 11770.746| |-----------------------------------------------------------------------------| r_work (final): 0.3361 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.123084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110256 restraints weight = 3128.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111025 restraints weight = 2726.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.111800 restraints weight = 2466.186| |-----------------------------------------------------------------------------| r_work (final): 0.3981 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.103254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099414 restraints weight = 791.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.100496 restraints weight = 357.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101396 restraints weight = 201.886| |-----------------------------------------------------------------------------| r_work (final): 0.3730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.058155 restraints weight = 9532.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059325 restraints weight = 3906.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.060008 restraints weight = 2372.420| |-----------------------------------------------------------------------------| r_work (final): 0.3038 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.070131 restraints weight = 9857.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069729 restraints weight = 5821.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070080 restraints weight = 5145.642| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 1.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 24268 Z= 0.336 Angle : 1.095 42.950 33658 Z= 0.582 Chirality : 0.055 0.406 3818 Planarity : 0.009 0.164 3470 Dihedral : 25.024 142.832 4884 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 31.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2328 helix: 0.07 (0.14), residues: 1374 sheet: -0.76 (0.31), residues: 240 loop : -1.67 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 319 HIS 0.003 0.001 HIS K 71 PHE 0.022 0.002 PHE C 124 TYR 0.022 0.001 TYR E 604 ARG 0.041 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.11995 ( 1093) hydrogen bonds : angle 5.48658 ( 3022) metal coordination : bond 0.03271 ( 24) metal coordination : angle 11.35731 ( 18) covalent geometry : bond 0.00744 (24244) covalent geometry : angle 1.06352 (33640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8617 (tt0) cc_final: 0.8328 (tp30) REVERT: A 360 MET cc_start: 0.8705 (mtm) cc_final: 0.8255 (mtm) REVERT: A 422 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8016 (pp20) REVERT: A 425 LEU cc_start: 0.8686 (mt) cc_final: 0.8449 (mt) REVERT: A 442 MET cc_start: 0.7511 (pmm) cc_final: 0.6202 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2044 time to fit residues: 17.7373 Evaluate side-chains 40 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.499 Evaluate side-chains 18 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1425 time to fit residues: 2.7801 Evaluate side-chains 14 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.078 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0089 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0334 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0467 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 100 optimal weight: 0.2980 chunk 233 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 204 optimal weight: 0.4980 chunk 198 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.093887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076661 restraints weight = 21671.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078150 restraints weight = 15252.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.079179 restraints weight = 11641.288| |-----------------------------------------------------------------------------| r_work (final): 0.3351 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.110146 restraints weight = 2962.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.110809 restraints weight = 2623.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.111366 restraints weight = 2415.358| |-----------------------------------------------------------------------------| r_work (final): 0.3980 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096679 restraints weight = 757.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098175 restraints weight = 438.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099184 restraints weight = 260.768| |-----------------------------------------------------------------------------| r_work (final): 0.3713 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058034 restraints weight = 9319.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059214 restraints weight = 3864.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059896 restraints weight = 2350.390| |-----------------------------------------------------------------------------| r_work (final): 0.3035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070491 restraints weight = 9924.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070141 restraints weight = 5649.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070753 restraints weight = 4600.859| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 1.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.163 24268 Z= 0.326 Angle : 1.034 15.735 33658 Z= 0.557 Chirality : 0.061 0.925 3818 Planarity : 0.010 0.244 3470 Dihedral : 25.073 142.683 4884 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2328 helix: -0.05 (0.14), residues: 1374 sheet: -0.82 (0.32), residues: 224 loop : -1.70 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.004 TRP E 182 HIS 0.002 0.000 HIS K 71 PHE 0.034 0.002 PHE A 575 TYR 0.017 0.001 TYR E 604 ARG 0.052 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.11781 ( 1093) hydrogen bonds : angle 5.47979 ( 3022) metal coordination : bond 0.03026 ( 24) metal coordination : angle 10.68366 ( 18) covalent geometry : bond 0.00760 (24244) covalent geometry : angle 1.00417 (33640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8582 (tt0) cc_final: 0.8276 (tp30) REVERT: A 325 MET cc_start: 0.8045 (ppp) cc_final: 0.7839 (ppp) REVERT: A 360 MET cc_start: 0.8741 (mtm) cc_final: 0.8299 (mtm) REVERT: A 422 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7946 (pp20) REVERT: A 425 LEU cc_start: 0.8678 (mt) cc_final: 0.8363 (mt) REVERT: A 442 MET cc_start: 0.7418 (pmm) cc_final: 0.6121 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1602 time to fit residues: 13.8271 Evaluate side-chains 39 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.538 Evaluate side-chains 19 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.074 Fit side-chains REVERT: K 62 THR cc_start: 0.7383 (p) cc_final: 0.6597 (p) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1728 time to fit residues: 3.5060 Evaluate side-chains 15 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.074 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0076 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0375 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0486 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 201 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 35 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 248 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.094303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077005 restraints weight = 21508.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078535 restraints weight = 14954.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079596 restraints weight = 11417.464| |-----------------------------------------------------------------------------| r_work (final): 0.3363 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.112939 restraints weight = 3384.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.114311 restraints weight = 2589.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115480 restraints weight = 2129.265| |-----------------------------------------------------------------------------| r_work (final): 0.3952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096365 restraints weight = 835.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098024 restraints weight = 474.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099154 restraints weight = 279.036| |-----------------------------------------------------------------------------| r_work (final): 0.3714 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058020 restraints weight = 9416.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059203 restraints weight = 3894.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059887 restraints weight = 2362.557| |-----------------------------------------------------------------------------| r_work (final): 0.3034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070468 restraints weight = 9742.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070188 restraints weight = 5697.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070553 restraints weight = 5343.528| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 1.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.231 24268 Z= 0.343 Angle : 1.059 26.463 33658 Z= 0.560 Chirality : 0.061 0.925 3818 Planarity : 0.010 0.244 3470 Dihedral : 25.073 142.683 4884 Min Nonbonded Distance : 0.784 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2328 helix: -0.05 (0.14), residues: 1374 sheet: -0.82 (0.32), residues: 224 loop : -1.70 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.004 TRP E 182 HIS 0.002 0.000 HIS I 71 PHE 0.034 0.002 PHE C 575 TYR 0.017 0.001 TYR E 604 ARG 0.052 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.11781 ( 1093) hydrogen bonds : angle 5.47979 ( 3022) metal coordination : bond 0.09783 ( 24) metal coordination : angle 14.54998 ( 18) covalent geometry : bond 0.00760 (24244) covalent geometry : angle 1.00417 (33640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8595 (tt0) cc_final: 0.8289 (tp30) REVERT: A 325 MET cc_start: 0.8059 (ppp) cc_final: 0.7838 (ppp) REVERT: A 360 MET cc_start: 0.8737 (mtm) cc_final: 0.8292 (mtm) REVERT: A 422 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7949 (pp20) REVERT: A 425 LEU cc_start: 0.8687 (mt) cc_final: 0.8370 (mt) REVERT: A 442 MET cc_start: 0.7424 (pmm) cc_final: 0.6125 (tpp) REVERT: A 587 ASN cc_start: 0.8640 (p0) cc_final: 0.8439 (p0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1575 time to fit residues: 13.5335 Evaluate side-chains 39 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.473 Evaluate side-chains 19 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1873 time to fit residues: 3.7652 Evaluate side-chains 15 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.065 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0066 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0400 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0394 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 159 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.094237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077179 restraints weight = 21607.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078656 restraints weight = 15158.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079675 restraints weight = 11648.821| |-----------------------------------------------------------------------------| r_work (final): 0.3362 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.126657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.112728 restraints weight = 3254.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.114111 restraints weight = 2512.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115187 restraints weight = 2089.190| |-----------------------------------------------------------------------------| r_work (final): 0.3947 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096459 restraints weight = 815.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098100 restraints weight = 462.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099169 restraints weight = 271.474| |-----------------------------------------------------------------------------| r_work (final): 0.3711 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058019 restraints weight = 9435.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059204 restraints weight = 3899.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059887 restraints weight = 2361.826| |-----------------------------------------------------------------------------| r_work (final): 0.3034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070484 restraints weight = 9874.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070130 restraints weight = 5660.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070688 restraints weight = 4594.647| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 1.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.231 24268 Z= 0.343 Angle : 1.059 26.463 33658 Z= 0.560 Chirality : 0.061 0.925 3818 Planarity : 0.010 0.244 3470 Dihedral : 25.073 142.683 4884 Min Nonbonded Distance : 0.784 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2328 helix: -0.05 (0.14), residues: 1374 sheet: -0.82 (0.32), residues: 224 loop : -1.70 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.004 TRP E 182 HIS 0.002 0.000 HIS I 71 PHE 0.034 0.002 PHE C 575 TYR 0.017 0.001 TYR C 604 ARG 0.052 0.001 ARG K 63 Details of bonding type rmsd hydrogen bonds : bond 0.11781 ( 1093) hydrogen bonds : angle 5.47979 ( 3022) metal coordination : bond 0.09783 ( 24) metal coordination : angle 14.54998 ( 18) covalent geometry : bond 0.00760 (24244) covalent geometry : angle 1.00417 (33640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8563 (tt0) cc_final: 0.8271 (tp30) REVERT: A 325 MET cc_start: 0.8052 (ppp) cc_final: 0.7848 (ppp) REVERT: A 360 MET cc_start: 0.8733 (mtm) cc_final: 0.8294 (mtm) REVERT: A 422 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7951 (pp20) REVERT: A 425 LEU cc_start: 0.8683 (mt) cc_final: 0.8367 (mt) REVERT: A 442 MET cc_start: 0.7406 (pmm) cc_final: 0.6109 (tpp) REVERT: A 587 ASN cc_start: 0.8637 (p0) cc_final: 0.8433 (p0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1973 time to fit residues: 16.5932 Evaluate side-chains 39 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.297 Evaluate side-chains 18 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1992 time to fit residues: 3.8976 Evaluate side-chains 15 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.083 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0084 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0513 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0453 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7999 > 50: distance: 0 - 1: 15.527 distance: 1 - 2: 24.579 distance: 2 - 3: 21.380 distance: 2 - 8: 18.162 distance: 3 - 4: 15.680 distance: 3 - 5: 20.209 distance: 5 - 6: 19.326 distance: 6 - 7: 21.721 distance: 7 - 8: 42.309 distance: 9 - 10: 13.241 distance: 9 - 11: 6.769 distance: 9 - 12: 17.091 distance: 12 - 13: 23.423 distance: 13 - 14: 48.202 distance: 14 - 15: 40.514 distance: 14 - 16: 22.570 distance: 15 - 19: 29.985 distance: 16 - 17: 58.190 distance: 16 - 18: 42.949 distance: 17 - 30: 27.593 distance: 18 - 19: 45.012 distance: 19 - 20: 19.392 distance: 20 - 21: 17.648 distance: 20 - 29: 4.499 distance: 21 - 22: 12.724 distance: 22 - 23: 10.952 distance: 23 - 29: 22.073 distance: 24 - 25: 11.996 distance: 24 - 26: 12.626 distance: 26 - 27: 12.920 distance: 27 - 28: 9.516 distance: 28 - 29: 18.925 distance: 30 - 31: 17.303 distance: 30 - 32: 14.445 distance: 30 - 33: 32.797 distance: 33 - 34: 6.823 distance: 34 - 35: 6.942 distance: 35 - 36: 17.956 distance: 35 - 37: 8.117 distance: 36 - 40: 27.798 distance: 37 - 38: 12.270 distance: 37 - 39: 16.960 distance: 38 - 49: 9.925 distance: 39 - 40: 18.991 distance: 40 - 41: 18.546 distance: 41 - 42: 21.301 distance: 41 - 48: 23.025 distance: 42 - 43: 30.915 distance: 42 - 44: 23.600 distance: 44 - 45: 47.275 distance: 45 - 46: 31.370 distance: 45 - 47: 43.269 distance: 47 - 48: 45.547 distance: 49 - 50: 8.913 distance: 49 - 51: 8.295 distance: 49 - 52: 6.819 distance: 52 - 53: 35.425 distance: 53 - 54: 45.858 distance: 54 - 55: 17.580 distance: 54 - 56: 17.807 distance: 55 - 59: 18.929 distance: 56 - 57: 11.835 distance: 56 - 58: 17.372 distance: 57 - 70: 17.713 distance: 58 - 59: 9.836 distance: 59 - 60: 27.264 distance: 60 - 61: 13.946 distance: 60 - 69: 17.171 distance: 61 - 62: 22.893 distance: 62 - 63: 42.353 distance: 63 - 64: 53.271 distance: 63 - 69: 47.166 distance: 64 - 65: 4.576 distance: 64 - 66: 56.360 distance: 66 - 67: 10.223 distance: 67 - 68: 18.419 distance: 68 - 69: 11.937 distance: 70 - 71: 27.099 distance: 70 - 72: 3.639 distance: 70 - 73: 8.705 distance: 73 - 74: 10.031