Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 06:38:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/04_2023/7xss_33433.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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 4 6.06 5 P 54 5.49 5 S 55 5.16 5 C 10509 2.51 5 N 2928 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 490": "OD1" <-> "OD2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 698": "OD1" <-> "OD2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 709": "OD1" <-> "OD2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1002": "OE1" <-> "OE2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1499": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B PHE 1524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1565": "OD1" <-> "OD2" Residue "B PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B GLU 1650": "OE1" <-> "OE2" Residue "B GLU 1657": "OE1" <-> "OE2" Residue "B TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1674": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 16847 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5361 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 3 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 438 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 10336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10336 Unusual residues: {' ZN': 4} Classifications: {'peptide': 1282, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 60, 'TRANS': 1221, None: 4} Not linked: pdbres="GLN B1692 " pdbres=" ZN B1801 " Not linked: pdbres=" ZN B1801 " pdbres=" ZN B1802 " Not linked: pdbres=" ZN B1802 " pdbres=" ZN B1803 " Not linked: pdbres=" ZN B1803 " pdbres=" ZN B1804 " Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10251 SG CYS B 491 51.531 61.380 43.574 1.00 60.61 S ATOM 10319 SG CYS B 501 52.869 59.111 41.007 1.00 78.43 S ATOM 10333 SG CYS B 503 50.624 62.101 39.975 1.00 63.44 S ATOM 10355 SG CYS B 506 54.129 62.759 41.028 1.00 61.94 S ATOM 12320 SG CYS B 750 37.086 68.987 69.699 1.00 82.00 S ATOM 12333 SG CYS B 752 35.703 72.353 68.473 1.00 76.41 S ATOM 12355 SG CYS B 755 39.381 71.473 67.865 1.00 66.60 S ATOM 14333 SG CYS B1018 40.584 94.375 98.167 1.00 72.20 S ATOM 14504 SG CYS B1406 40.785 90.807 97.058 1.00 61.86 S ATOM 14555 SG CYS B1414 37.418 92.784 96.977 1.00 67.22 S ATOM 14572 SG CYS B1417 40.053 93.446 94.418 1.00 58.03 S ATOM 7187 SG CYS B 88 73.014 51.784 19.001 1.00 75.41 S ATOM 7458 SG CYS B 121 75.863 50.427 16.716 1.00 90.38 S ATOM 7504 SG CYS B 127 75.564 54.021 17.405 1.00 77.54 S ATOM 7528 SG CYS B 130 76.582 51.697 20.272 1.00 72.67 S Time building chain proxies: 9.22, per 1000 atoms: 0.55 Number of scatterers: 16847 At special positions: 0 Unit cell: (107.67, 152.29, 132.89, 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 4 29.99 S 55 16.00 P 54 15.00 O 3297 8.00 N 2928 7.00 C 10509 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: 6.97 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 506 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 752 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1406 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 130 " Number of angles added : 21 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 39.4% alpha, 16.9% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.668A pdb=" N ASN C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 59 removed outlier: 4.053A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.625A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 110 removed outlier: 4.095A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.920A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.330A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.674A pdb=" N GLN C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.796A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.543A pdb=" N LYS C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 474 removed outlier: 3.684A pdb=" N PHE C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.551A pdb=" N GLY C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.694A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.744A pdb=" N LEU C 611 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.766A pdb=" N GLY C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 677 removed outlier: 3.570A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 677 " --> pdb=" O ILE C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 4.472A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 692 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.652A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.682A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.528A pdb=" N ALA B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.703A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.565A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 617 through 624 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.523A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 Processing helix chain 'B' and resid 752 through 758 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.618A pdb=" N GLU B 779 " --> pdb=" O ASN B 776 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 780' Processing helix chain 'B' and resid 831 through 848 removed outlier: 3.840A pdb=" N GLY B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 removed outlier: 3.613A pdb=" N GLY B 859 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 removed outlier: 3.790A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.724A pdb=" N ASP B 914 " --> pdb=" O SER B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.901A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.595A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B1399 " --> pdb=" O LEU B1395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1394 through 1399' Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.249A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.972A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B1493 " --> pdb=" O ILE B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1501 removed outlier: 4.147A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1501 " --> pdb=" O ILE B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1552 through 1556 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.558A pdb=" N GLY B1603 " --> pdb=" O ILE B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.662A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'C' and resid 425 through 431 Processing sheet with id=AA2, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.355A pdb=" N LEU C 580 " --> pdb=" O ILE C 623 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY C 625 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 582 " --> pdb=" O GLY C 625 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N CYS C 627 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 626 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 181 removed outlier: 4.230A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 11 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 238 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.268A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.690A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.579A pdb=" N SER B 517 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 533 removed outlier: 10.509A pdb=" N GLU B 526 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASP B 547 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ARG B 528 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 545 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ARG B 530 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N GLY B 543 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 532 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 865 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 787 through 792 removed outlier: 6.446A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 951 " --> pdb=" O THR B1569 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B1569 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 953 " --> pdb=" O LEU B1567 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B1567 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 955 " --> pdb=" O ASP B1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 967 through 968 removed outlier: 4.449A pdb=" N LYS B 988 " --> pdb=" O ASP B 968 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 989 " --> pdb=" O GLU B1510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1421 through 1422 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 7.56 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: 5262 1.34 - 1.46: 3315 1.46 - 1.58: 8572 1.58 - 1.70: 107 1.70 - 1.82: 76 Bond restraints: 17332 Sorted by residual: bond pdb=" CA ASN B 973 " pdb=" CB ASN B 973 " ideal model delta sigma weight residual 1.528 1.576 -0.048 1.67e-02 3.59e+03 8.20e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" N ASN B1544 " pdb=" CA ASN B1544 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C ARG B1644 " pdb=" N TYR B1645 " ideal model delta sigma weight residual 1.333 1.374 -0.041 2.74e-02 1.33e+03 2.26e+00 bond pdb=" CB ASP B1565 " pdb=" CG ASP B1565 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 17327 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.01: 580 106.01 - 113.00: 9229 113.00 - 119.99: 6141 119.99 - 126.98: 7357 126.98 - 133.97: 320 Bond angle restraints: 23627 Sorted by residual: angle pdb=" CA PRO B 86 " pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 112.00 102.06 9.94 1.40e+00 5.10e-01 5.04e+01 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 113.10 109.69 3.41 9.70e-01 1.06e+00 1.24e+01 angle pdb=" CA GLU B1496 " pdb=" CB GLU B1496 " pdb=" CG GLU B1496 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA GLU C 268 " pdb=" CB GLU C 268 " pdb=" CG GLU C 268 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ASP B1471 " pdb=" C ASP B1471 " pdb=" N GLU B1472 " ideal model delta sigma weight residual 116.84 122.20 -5.36 1.71e+00 3.42e-01 9.83e+00 ... (remaining 23622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9877 35.92 - 71.83: 391 71.83 - 107.74: 21 107.74 - 143.66: 0 143.66 - 179.57: 4 Dihedral angle restraints: 10293 sinusoidal: 4700 harmonic: 5593 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 43.53 156.47 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 51.57 -179.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D -14 " pdb=" C1' U D -14 " pdb=" N1 U D -14 " pdb=" C2 U D -14 " ideal model delta sinusoidal sigma weight residual -128.00 47.29 -175.29 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 10290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1936 0.040 - 0.079: 473 0.079 - 0.119: 136 0.119 - 0.158: 18 0.158 - 0.198: 3 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C1' A D -16 " pdb=" O4' A D -16 " pdb=" C2' A D -16 " pdb=" N9 A D -16 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASN B1544 " pdb=" N ASN B1544 " pdb=" C ASN B1544 " pdb=" CB ASN B1544 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 2563 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 85 " -0.097 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO B 86 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 439 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 440 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 37 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO C 38 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.035 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 452 2.69 - 3.25: 15678 3.25 - 3.80: 25665 3.80 - 4.35: 33989 4.35 - 4.90: 56432 Nonbonded interactions: 132216 Sorted by model distance: nonbonded pdb=" O ALA C 626 " pdb=" OG1 THR C 660 " model vdw 2.143 2.440 nonbonded pdb=" NZ LYS B1571 " pdb=" OD1 ASN B1573 " model vdw 2.145 2.520 nonbonded pdb=" OP2 U D 6 " pdb=" OG SER B 854 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR B1436 " pdb=" OE2 GLU B1441 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR B 191 " pdb=" OD2 ASP B 386 " model vdw 2.174 2.440 ... (remaining 132211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 6.060 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.490 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.135 17332 Z= 0.196 Angle : 0.613 10.265 23627 Z= 0.346 Chirality : 0.039 0.198 2566 Planarity : 0.005 0.138 2844 Dihedral : 17.989 179.575 6699 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer Outliers : 0.59 % 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: -0.24 (0.19), residues: 1924 helix: 1.43 (0.21), residues: 630 sheet: 0.88 (0.32), residues: 270 loop : -1.57 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 365 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 370 average time/residue: 0.3605 time to fit residues: 188.0835 Evaluate side-chains 349 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2385 time to fit residues: 4.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN C 612 ASN B 112 GLN B 335 GLN B 615 ASN B 668 GLN B1438 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 17332 Z= 0.422 Angle : 0.655 7.972 23627 Z= 0.343 Chirality : 0.046 0.251 2566 Planarity : 0.006 0.087 2844 Dihedral : 11.835 177.904 2745 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 5.22 % 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: -0.44 (0.19), residues: 1924 helix: 1.21 (0.20), residues: 640 sheet: 0.51 (0.33), residues: 255 loop : -1.56 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 396 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 52 residues processed: 443 average time/residue: 0.3656 time to fit residues: 232.1180 Evaluate side-chains 411 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 359 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.1776 time to fit residues: 19.3262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 123 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 145 optimal weight: 0.0040 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS C 415 ASN C 514 HIS C 553 ASN B 335 GLN B1438 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 17332 Z= 0.150 Angle : 0.521 6.569 23627 Z= 0.272 Chirality : 0.040 0.181 2566 Planarity : 0.004 0.069 2844 Dihedral : 11.709 178.902 2745 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 2.05 % 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: -0.15 (0.19), residues: 1924 helix: 1.58 (0.20), residues: 641 sheet: 0.54 (0.33), residues: 253 loop : -1.44 (0.18), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 376 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 393 average time/residue: 0.3499 time to fit residues: 196.3240 Evaluate side-chains 382 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 364 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2263 time to fit residues: 9.2238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 181 optimal weight: 0.1980 chunk 192 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 553 ASN B 973 ASN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.184 Angle : 0.521 7.759 23627 Z= 0.271 Chirality : 0.040 0.185 2566 Planarity : 0.004 0.065 2844 Dihedral : 11.685 179.406 2745 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.46 % 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: -0.09 (0.19), residues: 1924 helix: 1.68 (0.20), residues: 641 sheet: 0.50 (0.33), residues: 255 loop : -1.42 (0.18), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 385 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 402 average time/residue: 0.3518 time to fit residues: 202.0650 Evaluate side-chains 392 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 372 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1765 time to fit residues: 9.0389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 132 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 17332 Z= 0.339 Angle : 0.608 7.855 23627 Z= 0.317 Chirality : 0.044 0.235 2566 Planarity : 0.005 0.062 2844 Dihedral : 11.867 178.377 2745 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 3.34 % 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: -0.22 (0.19), residues: 1924 helix: 1.50 (0.20), residues: 641 sheet: 0.60 (0.34), residues: 245 loop : -1.48 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 394 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 426 average time/residue: 0.3625 time to fit residues: 221.3462 Evaluate side-chains 403 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 369 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2005 time to fit residues: 14.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 612 ASN B 498 GLN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.204 Angle : 0.554 7.057 23627 Z= 0.289 Chirality : 0.041 0.214 2566 Planarity : 0.005 0.058 2844 Dihedral : 11.827 178.859 2745 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.76 % 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: -0.11 (0.19), residues: 1924 helix: 1.66 (0.20), residues: 640 sheet: 0.57 (0.34), residues: 245 loop : -1.42 (0.19), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 389 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 407 average time/residue: 0.3462 time to fit residues: 201.6867 Evaluate side-chains 400 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 384 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1925 time to fit residues: 8.1123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17332 Z= 0.279 Angle : 0.592 10.083 23627 Z= 0.307 Chirality : 0.043 0.223 2566 Planarity : 0.005 0.060 2844 Dihedral : 11.860 178.718 2745 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 1.99 % 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: -0.11 (0.19), residues: 1924 helix: 1.63 (0.20), residues: 641 sheet: 0.56 (0.34), residues: 245 loop : -1.41 (0.19), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 399 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 416 average time/residue: 0.3518 time to fit residues: 209.3690 Evaluate side-chains 402 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 382 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1953 time to fit residues: 9.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS C 612 ASN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17332 Z= 0.217 Angle : 0.564 6.438 23627 Z= 0.295 Chirality : 0.041 0.210 2566 Planarity : 0.005 0.060 2844 Dihedral : 11.850 178.991 2745 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.17 % 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: -0.05 (0.19), residues: 1924 helix: 1.75 (0.20), residues: 640 sheet: 0.58 (0.34), residues: 245 loop : -1.41 (0.19), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 386 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 392 average time/residue: 0.3534 time to fit residues: 197.3566 Evaluate side-chains 395 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 384 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1963 time to fit residues: 6.4561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 169 optimal weight: 0.0030 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN C 133 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17332 Z= 0.232 Angle : 0.571 6.630 23627 Z= 0.297 Chirality : 0.041 0.206 2566 Planarity : 0.005 0.062 2844 Dihedral : 11.853 179.220 2745 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.82 % 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: -0.06 (0.19), residues: 1924 helix: 1.74 (0.20), residues: 640 sheet: 0.55 (0.34), residues: 245 loop : -1.42 (0.19), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 383 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 388 average time/residue: 0.3656 time to fit residues: 202.8772 Evaluate side-chains 384 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 377 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2201 time to fit residues: 5.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 182 optimal weight: 0.0870 chunk 157 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 HIS C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.172 Angle : 0.548 6.609 23627 Z= 0.285 Chirality : 0.040 0.196 2566 Planarity : 0.005 0.062 2844 Dihedral : 11.789 179.988 2745 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.35 % 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: 0.06 (0.19), residues: 1924 helix: 1.89 (0.21), residues: 634 sheet: 0.57 (0.34), residues: 245 loop : -1.35 (0.19), residues: 1045 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 385 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 387 average time/residue: 0.3704 time to fit residues: 203.3824 Evaluate side-chains 380 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3132 time to fit residues: 4.0731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107763 restraints weight = 24266.374| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.07 r_work: 0.3176 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17332 Z= 0.246 Angle : 0.579 6.550 23627 Z= 0.302 Chirality : 0.042 0.203 2566 Planarity : 0.005 0.063 2844 Dihedral : 11.831 179.830 2745 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.53 % 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: 0.01 (0.19), residues: 1924 helix: 1.83 (0.21), residues: 635 sheet: 0.58 (0.34), residues: 245 loop : -1.38 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 4536.63 seconds wall clock time: 82 minutes 19.34 seconds (4939.34 seconds total)