Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 04:59:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/04_2023/7dok_30795_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 7141 2.51 5 N 1942 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11534 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "T" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 7457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7457 Classifications: {'peptide': 925} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 894} Chain: "B" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1214 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 149} Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "G" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1360 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 1 Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'HCU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 25 Unusual residues: {' MG': 3, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 7, 'water': 2} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3367 SG CYS A 301 90.773 66.447 46.517 1.00 23.11 S ATOM 3408 SG CYS A 306 90.854 65.667 42.318 1.00 23.19 S ATOM 3440 SG CYS A 310 94.122 65.636 44.859 1.00 20.66 S ATOM 4848 SG CYS A 487 72.617 61.166 54.936 1.00 29.89 S ATOM 6101 SG CYS A 645 71.622 60.925 50.803 1.00 32.78 S ATOM 6107 SG CYS A 646 74.723 63.422 52.381 1.00 31.19 S Time building chain proxies: 6.69, per 1000 atoms: 0.58 Number of scatterers: 11534 At special positions: 0 Unit cell: (150.729, 94.072, 131.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 81 16.00 P 49 15.00 Mg 4 11.99 O 2315 8.00 N 1942 7.00 C 7141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 46.0% alpha, 11.0% beta 20 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.533A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.638A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.526A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.078A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.382A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.700A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 455 removed outlier: 4.177A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.772A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.688A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.676A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 856 through 871 removed outlier: 3.528A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.903A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.206A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 removed outlier: 4.120A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 97 removed outlier: 3.584A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.826A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.772A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 36 through 98 removed outlier: 3.657A pdb=" N LYS G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.820A pdb=" N ILE G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.799A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= D, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.487A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= G, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.245A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.693A pdb=" N GLN G 158 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2573 1.33 - 1.45: 2813 1.45 - 1.57: 6254 1.57 - 1.69: 90 1.69 - 1.81: 127 Bond restraints: 11857 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.650 1.429 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 HCU P1201 " pdb=" O1 HCU P1201 " ideal model delta sigma weight residual 1.184 1.401 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.400 1.222 0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.510 1.338 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 1.527 1.375 0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 95.75 - 104.20: 319 104.20 - 112.64: 6244 112.64 - 121.09: 6635 121.09 - 129.54: 2988 129.54 - 137.98: 89 Bond angle restraints: 16275 Sorted by residual: angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 109.47 132.79 -23.32 3.00e+00 1.11e-01 6.04e+01 angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.86 -10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" C2' G P 8 " pdb=" C1' G P 8 " pdb=" N9 G P 8 " ideal model delta sigma weight residual 112.00 101.41 10.59 1.50e+00 4.44e-01 4.98e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 118.46 137.98 -19.52 3.00e+00 1.11e-01 4.23e+01 ... (remaining 16270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 6540 21.47 - 42.94: 426 42.94 - 64.41: 33 64.41 - 85.89: 8 85.89 - 107.36: 3 Dihedral angle restraints: 7010 sinusoidal: 3078 harmonic: 3932 Sorted by residual: dihedral pdb=" O4 POP A1007 " pdb=" O POP A1007 " pdb=" P2 POP A1007 " pdb=" P1 POP A1007 " ideal model delta sinusoidal sigma weight residual -57.41 -164.77 107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C4' U P 7 " pdb=" C3' U P 7 " pdb=" C2' U P 7 " pdb=" C1' U P 7 " ideal model delta sinusoidal sigma weight residual 36.00 3.53 32.47 1 8.00e+00 1.56e-02 2.35e+01 dihedral pdb=" O4 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " pdb=" P1 POP A1003 " ideal model delta sinusoidal sigma weight residual -57.41 28.41 -85.82 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 7007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1861 0.316 - 0.631: 0 0.631 - 0.947: 0 0.947 - 1.262: 0 1.262 - 1.578: 1 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.74 -1.16 -1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1' G P 8 " pdb=" O4' G P 8 " pdb=" C2' G P 8 " pdb=" N9 G P 8 " both_signs ideal model delta sigma weight residual False 2.46 2.72 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1859 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " 0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASP A 155 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP A 155 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 156 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 8 " 0.011 2.00e-02 2.50e+03 2.18e-02 1.43e+01 pdb=" N9 G P 8 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G P 8 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G P 8 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G P 8 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 G P 8 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G P 8 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G P 8 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.044 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO B 178 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.037 5.00e-02 4.00e+02 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 19 2.34 - 2.98: 5204 2.98 - 3.62: 17240 3.62 - 4.26: 28629 4.26 - 4.90: 45728 Nonbonded interactions: 96820 Sorted by model distance: nonbonded pdb=" O4 POP A1003 " pdb=" O HOH A1101 " model vdw 1.695 2.440 nonbonded pdb="MG MG A1005 " pdb=" O6 POP A1007 " model vdw 1.731 2.170 nonbonded pdb="MG MG A1006 " pdb=" O2 POP A1007 " model vdw 1.950 2.170 nonbonded pdb=" O PHE A 77 " pdb=" OE1 GLN A 81 " model vdw 2.035 3.040 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1005 " model vdw 2.052 2.170 ... (remaining 96815 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 'B' selection = (chain 'G' and resid 37 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.000 Extract box with map and model: 5.330 Check model and map are aligned: 0.200 Set scattering table: 0.100 Process input model: 38.050 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.009 0.221 11857 Z= 0.542 Angle : 1.015 23.323 16275 Z= 0.648 Chirality : 0.072 1.578 1862 Planarity : 0.006 0.065 1914 Dihedral : 13.348 107.357 4464 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1313 helix: -1.65 (0.17), residues: 651 sheet: -0.82 (0.41), residues: 148 loop : -1.51 (0.23), residues: 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 1.327 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 1.0840 time to fit residues: 243.0997 Evaluate side-chains 141 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.1712 time to fit residues: 3.0504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN A 75 HIS A 117 GLN A 541 GLN A 691 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN B 105 ASN B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 65 GLN G 100 ASN G 179 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 11857 Z= 0.147 Angle : 0.498 6.080 16275 Z= 0.265 Chirality : 0.038 0.142 1862 Planarity : 0.004 0.050 1914 Dihedral : 6.986 126.744 1973 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.86 (0.21), residues: 1313 helix: -0.23 (0.19), residues: 649 sheet: -0.53 (0.43), residues: 127 loop : -0.83 (0.25), residues: 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.313 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 169 average time/residue: 0.9836 time to fit residues: 184.3108 Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3357 time to fit residues: 3.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 541 GLN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11857 Z= 0.175 Angle : 0.491 9.994 16275 Z= 0.258 Chirality : 0.039 0.139 1862 Planarity : 0.003 0.046 1914 Dihedral : 6.515 122.428 1973 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.32 (0.22), residues: 1313 helix: 0.24 (0.20), residues: 656 sheet: -0.38 (0.42), residues: 132 loop : -0.58 (0.26), residues: 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.433 Fit side-chains outliers start: 41 outliers final: 16 residues processed: 173 average time/residue: 1.0276 time to fit residues: 196.9904 Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.4062 time to fit residues: 5.8078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 81 optimal weight: 0.0010 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 541 GLN A 642 HIS A 892 HIS B 104 ASN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 11857 Z= 0.358 Angle : 0.578 9.202 16275 Z= 0.302 Chirality : 0.043 0.163 1862 Planarity : 0.004 0.042 1914 Dihedral : 6.874 121.993 1973 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.42 (0.22), residues: 1313 helix: 0.17 (0.20), residues: 657 sheet: -0.60 (0.41), residues: 136 loop : -0.60 (0.26), residues: 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.211 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 163 average time/residue: 1.1450 time to fit residues: 206.2734 Evaluate side-chains 151 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 0.3650 time to fit residues: 6.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 543 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 104 ASN B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 11857 Z= 0.134 Angle : 0.475 8.241 16275 Z= 0.247 Chirality : 0.038 0.135 1862 Planarity : 0.003 0.043 1914 Dihedral : 6.287 116.866 1973 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.02 (0.23), residues: 1313 helix: 0.54 (0.20), residues: 658 sheet: -0.47 (0.41), residues: 134 loop : -0.37 (0.27), residues: 521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 168 average time/residue: 1.0209 time to fit residues: 190.3287 Evaluate side-chains 146 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1811 time to fit residues: 2.6619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 0.0070 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 11857 Z= 0.161 Angle : 0.483 7.994 16275 Z= 0.250 Chirality : 0.038 0.170 1862 Planarity : 0.003 0.048 1914 Dihedral : 6.171 114.997 1973 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.22 (0.23), residues: 1313 helix: 0.71 (0.21), residues: 654 sheet: -0.41 (0.40), residues: 134 loop : -0.28 (0.27), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.373 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 163 average time/residue: 1.0566 time to fit residues: 190.7245 Evaluate side-chains 151 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.1734 time to fit residues: 3.0283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 11857 Z= 0.138 Angle : 0.476 7.605 16275 Z= 0.246 Chirality : 0.038 0.152 1862 Planarity : 0.003 0.047 1914 Dihedral : 6.040 113.325 1973 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.38 (0.23), residues: 1313 helix: 0.84 (0.21), residues: 657 sheet: -0.25 (0.41), residues: 134 loop : -0.21 (0.27), residues: 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.291 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 167 average time/residue: 1.0425 time to fit residues: 192.5385 Evaluate side-chains 157 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.3887 time to fit residues: 4.2419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11857 Z= 0.159 Angle : 0.488 12.065 16275 Z= 0.249 Chirality : 0.038 0.148 1862 Planarity : 0.003 0.048 1914 Dihedral : 6.053 113.421 1973 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.43 (0.23), residues: 1313 helix: 0.90 (0.21), residues: 654 sheet: -0.22 (0.41), residues: 134 loop : -0.21 (0.27), residues: 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.313 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 164 average time/residue: 1.0917 time to fit residues: 198.2041 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.9114 time to fit residues: 4.7810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5562 > 50: distance: 100 - 102: 9.459 distance: 102 - 103: 6.168 distance: 103 - 104: 19.019 distance: 103 - 106: 17.781 distance: 104 - 105: 33.535 distance: 104 - 110: 10.971 distance: 106 - 107: 9.444 distance: 107 - 108: 22.798 distance: 107 - 109: 22.166 distance: 110 - 111: 25.613 distance: 111 - 112: 7.572 distance: 112 - 113: 35.816 distance: 112 - 115: 14.034 distance: 115 - 116: 22.167 distance: 116 - 117: 26.743 distance: 116 - 119: 37.014 distance: 117 - 118: 26.780 distance: 117 - 122: 12.620 distance: 119 - 120: 15.764 distance: 122 - 123: 5.692 distance: 123 - 124: 17.394 distance: 123 - 126: 17.190 distance: 124 - 125: 14.439 distance: 124 - 129: 13.753 distance: 125 - 151: 34.137 distance: 126 - 127: 19.716 distance: 126 - 128: 13.788 distance: 129 - 130: 7.730 distance: 130 - 131: 8.711 distance: 130 - 133: 14.560 distance: 131 - 132: 6.353 distance: 131 - 134: 6.184 distance: 132 - 159: 13.926 distance: 134 - 135: 3.071 distance: 135 - 136: 6.605 distance: 136 - 137: 7.400 distance: 136 - 146: 10.878 distance: 137 - 165: 7.599 distance: 138 - 139: 5.684 distance: 139 - 140: 10.639 distance: 139 - 141: 9.624 distance: 140 - 142: 20.265 distance: 141 - 143: 4.622 distance: 142 - 144: 5.046 distance: 144 - 145: 11.968 distance: 147 - 148: 6.184 distance: 147 - 150: 3.798 distance: 148 - 149: 9.216 distance: 149 - 172: 12.710 distance: 151 - 152: 4.129 distance: 152 - 153: 3.884 distance: 152 - 155: 8.593 distance: 153 - 154: 6.884 distance: 153 - 159: 4.720 distance: 154 - 179: 3.223 distance: 155 - 156: 5.379 distance: 156 - 157: 9.963 distance: 156 - 158: 10.605 distance: 159 - 160: 13.937 distance: 160 - 161: 9.800 distance: 160 - 163: 14.679 distance: 161 - 162: 8.194 distance: 161 - 165: 9.476 distance: 162 - 185: 4.459 distance: 163 - 164: 15.312 distance: 165 - 166: 7.395 distance: 166 - 167: 8.016 distance: 166 - 169: 10.511 distance: 167 - 168: 12.377 distance: 167 - 172: 7.685 distance: 168 - 193: 16.705 distance: 169 - 170: 8.546 distance: 169 - 171: 12.620