Starting phenix.real_space_refine on Wed Dec 13 01:14:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_28034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_28034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_28034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_28034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8edg_28034/12_2023/8edg_28034.pdb" } 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 Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 206": "OD1" <-> "OD2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 584": "OE1" <-> "OE2" Residue "G PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 36": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.35, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.92 Conformation dependent library (CDL) restraints added in 3.6 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: 9.09 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: 9.15 Time building geometry restraints manager: 11.44 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: 98.81 - 105.88: 1385 105.88 - 112.94: 13348 112.94 - 120.01: 8659 120.01 - 127.08: 9579 127.08 - 134.15: 669 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 2.440 nonbonded pdb=" OG SER A 87 " pdb=" OD1 ASP A 89 " model vdw 2.177 2.440 nonbonded pdb=" O ASP G 173 " pdb=" NZ LYS G 244 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR E 604 " pdb=" OE1 GLN G 100 " model vdw 2.217 2.440 nonbonded pdb=" OP1 DA Q 29 " pdb=" NZ LYS C 72 " model vdw 2.218 2.520 ... (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 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.490 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 74.200 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.720 ------------------------------------------------------------------------------- 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 24244 Z= 0.169 Angle : 0.607 9.616 33640 Z= 0.344 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.564 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1434 time to fit residues: 13.7855 Evaluate side-chains 42 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7972 Evaluate side-chains 20 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1111 time to fit residues: 2.4448 Evaluate side-chains 7 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0992 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0539 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0122 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0487 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0162 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 229 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 416 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 1.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24244 Z= 0.240 Angle : 0.761 7.907 33640 Z= 0.444 Chirality : 0.045 0.299 3818 Planarity : 0.005 0.048 3470 Dihedral : 24.961 141.257 4884 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 1.03 % Allowed : 4.55 % Favored : 94.42 % Rotamer: Outliers : 1.49 % Allowed : 5.86 % Favored : 92.66 % 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 (0.17), residues: 2328 helix: 0.62 (0.14), residues: 1382 sheet: -0.88 (0.31), residues: 240 loop : -1.55 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 319 HIS 0.007 0.001 HIS E 134 PHE 0.026 0.002 PHE E 124 TYR 0.016 0.001 TYR E 131 ARG 0.005 0.001 ARG E 306 *********************** 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 80 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 79 average time/residue: 0.1593 time to fit residues: 16.4064 Evaluate side-chains 44 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0413 time to fit residues: 0.8178 Evaluate side-chains 31 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2006 time to fit residues: 6.5106 Evaluate side-chains 15 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1111 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0077 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0396 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0127 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0433 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 204 optimal weight: 0.0870 chunk 228 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 184 optimal weight: 10.0000 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 14 ASN K 15 GLN Total number of N/Q/H flips: 2 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 1.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.257 24244 Z= 0.410 Angle : 0.993 29.051 33640 Z= 0.553 Chirality : 0.056 0.478 3818 Planarity : 0.008 0.121 3470 Dihedral : 25.042 141.890 4884 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % Rotamer: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % 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: -0.84 (0.17), residues: 2328 helix: 0.15 (0.14), residues: 1398 sheet: -0.79 (0.31), residues: 240 loop : -1.76 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 319 HIS 0.003 0.001 HIS E 134 PHE 0.020 0.002 PHE C 371 TYR 0.009 0.001 TYR C 436 ARG 0.044 0.001 ARG K 63 *********************** 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 69 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.2107 time to fit residues: 17.9965 Evaluate side-chains 36 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7041 Evaluate side-chains 22 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2278 time to fit residues: 5.2739 Evaluate side-chains 15 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1016 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0081 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0372 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0127 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0487 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 7.9990 chunk 173 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 1.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.257 24244 Z= 0.410 Angle : 0.993 29.050 33640 Z= 0.553 Chirality : 0.056 0.478 3818 Planarity : 0.008 0.121 3470 Dihedral : 25.042 141.890 4884 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % 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: -0.84 (0.17), residues: 2328 helix: 0.15 (0.14), residues: 1398 sheet: -0.79 (0.31), residues: 240 loop : -1.76 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 319 HIS 0.003 0.001 HIS E 134 PHE 0.020 0.002 PHE C 371 TYR 0.009 0.001 TYR A 436 ARG 0.044 0.001 ARG K 63 *********************** 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 62 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1649 time to fit residues: 13.3743 Evaluate side-chains 39 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7434 Evaluate side-chains 21 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1303 time to fit residues: 2.9756 Evaluate side-chains 15 residues out of total 68 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.076 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0071 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0397 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0139 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0454 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4851 > 50: distance: 0 - 1: 4.412 distance: 2 - 3: 3.423 distance: 2 - 4: 3.951 distance: 3 - 7: 3.356 distance: 4 - 5: 4.674 distance: 5 - 16: 24.850 distance: 7 - 8: 5.040 distance: 8 - 9: 3.184 distance: 8 - 15: 22.931 distance: 9 - 10: 14.669 distance: 11 - 12: 5.708 distance: 12 - 13: 10.077 distance: 12 - 14: 16.677 distance: 14 - 15: 35.896 distance: 16 - 17: 46.053 distance: 16 - 18: 42.113 distance: 16 - 19: 41.989 distance: 19 - 20: 24.473 distance: 20 - 21: 29.832 distance: 21 - 22: 18.298 distance: 21 - 23: 28.929 distance: 22 - 26: 11.393 distance: 23 - 24: 66.607 distance: 23 - 25: 40.489 distance: 24 - 37: 36.039 distance: 25 - 26: 27.295 distance: 26 - 27: 13.980 distance: 27 - 28: 7.851 distance: 27 - 36: 9.916 distance: 28 - 29: 4.898 distance: 29 - 30: 26.488 distance: 30 - 31: 13.456 distance: 30 - 36: 21.037 distance: 31 - 32: 5.471 distance: 31 - 33: 21.323 distance: 33 - 34: 24.712 distance: 34 - 35: 3.902 distance: 35 - 36: 10.821 distance: 37 - 38: 8.825 distance: 37 - 39: 17.534 distance: 37 - 40: 21.757 distance: 40 - 41: 14.743 distance: 41 - 42: 44.111 distance: 42 - 43: 36.262 distance: 42 - 44: 18.295 distance: 43 - 47: 41.319 distance: 44 - 45: 13.159 distance: 44 - 46: 19.708 distance: 45 - 58: 21.113 distance: 46 - 47: 30.498 distance: 47 - 48: 41.375 distance: 48 - 49: 17.006 distance: 48 - 57: 50.476 distance: 49 - 50: 28.510 distance: 50 - 51: 63.697 distance: 51 - 52: 57.274 distance: 51 - 57: 50.080 distance: 52 - 53: 42.614 distance: 52 - 54: 34.164 distance: 54 - 55: 23.242 distance: 55 - 56: 34.763 distance: 56 - 57: 43.793 distance: 58 - 59: 19.175 distance: 58 - 60: 15.792 distance: 58 - 61: 13.467 distance: 61 - 62: 18.106 distance: 62 - 63: 20.745 distance: 63 - 64: 20.919 distance: 63 - 65: 29.046 distance: 64 - 68: 20.337 distance: 65 - 66: 13.278 distance: 65 - 67: 14.140 distance: 66 - 80: 30.722 distance: 67 - 68: 17.586 distance: 68 - 69: 38.999 distance: 69 - 70: 22.985 distance: 69 - 79: 8.842 distance: 70 - 71: 8.078 distance: 71 - 72: 14.992 distance: 72 - 73: 22.661 distance: 72 - 79: 8.618 distance: 73 - 74: 32.606 distance: 73 - 75: 19.925 distance: 75 - 76: 31.723 distance: 76 - 77: 34.096 distance: 76 - 78: 33.622 distance: 78 - 79: 39.913 distance: 80 - 81: 10.823 distance: 80 - 82: 3.539 distance: 80 - 83: 13.142 distance: 83 - 84: 14.540 distance: 84 - 85: 20.370 distance: 85 - 86: 32.688 distance: 85 - 87: 12.947 distance: 86 - 90: 24.542 distance: 87 - 88: 13.826 distance: 87 - 89: 19.709 distance: 88 - 100: 8.563 distance: 89 - 90: 15.942 distance: 90 - 91: 17.433 distance: 91 - 92: 18.080 distance: 91 - 99: 21.249 distance: 92 - 93: 31.710 distance: 92 - 94: 23.861 distance: 94 - 95: 7.869 distance: 95 - 96: 9.902 distance: 95 - 97: 8.428 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