Starting phenix.real_space_refine on Mon Mar 18 19:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glk_40196/03_2024/8glk_40196_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13852 2.51 5 N 3661 2.21 5 O 4340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 221": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A GLU 1670": "OE1" <-> "OE2" Residue "A PHE 1731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1990": "OE1" <-> "OE2" Residue "A TYR 2372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21899 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.30, per 1000 atoms: 0.52 Number of scatterers: 21899 At special positions: 0 Unit cell: (122.304, 128.96, 143.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 4340 8.00 N 3661 7.00 C 13852 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: 8.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 30 sheets defined 11.2% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 305 removed outlier: 4.602A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.859A pdb=" N ARG A 661 " --> pdb=" O ASN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 removed outlier: 4.134A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 811 through 818 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.089A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1578 through 1580 No H-bonds generated for 'chain 'A' and resid 1578 through 1580' Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1628 Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1831 through 1833 No H-bonds generated for 'chain 'A' and resid 1831 through 1833' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1977 through 1980 No H-bonds generated for 'chain 'A' and resid 1977 through 1980' Processing helix chain 'A' and resid 1988 through 1994 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.788A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2148 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.768A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 306 removed outlier: 3.811A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.929A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 551 through 553 Processing sheet with id= B, first strand: chain 'D' and resid 605 through 613 Processing sheet with id= C, first strand: chain 'A' and resid 763 through 767 removed outlier: 6.629A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A1640 " --> pdb=" O PRO A1585 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE A1662 " --> pdb=" O GLY A1641 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A1643 " --> pdb=" O PHE A1660 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE A1660 " --> pdb=" O ARG A1643 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR A1693 " --> pdb=" O SER A1727 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER A1727 " --> pdb=" O THR A1693 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A1771 " --> pdb=" O SER A1727 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A1729 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A1769 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A1731 " --> pdb=" O GLN A1767 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN A1767 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR A1733 " --> pdb=" O ASN A1765 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A1765 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE A1735 " --> pdb=" O ALA A1763 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A1763 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A2348 " --> pdb=" O THR A2334 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 141 " --> pdb=" O PHE A2401 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A 224 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A 240 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 152 Processing sheet with id= E, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= F, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= G, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.909A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 425 through 428 removed outlier: 5.829A pdb=" N LEU A 503 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 347 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 505 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= K, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= L, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= M, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.656A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1250 through 1254 Processing sheet with id= O, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= P, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= Q, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= R, first strand: chain 'A' and resid 1342 through 1348 Processing sheet with id= S, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.322A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 1739 through 1742 Processing sheet with id= U, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= V, first strand: chain 'A' and resid 2027 through 2032 removed outlier: 6.194A pdb=" N GLU A2258 " --> pdb=" O LYS A2198 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A2200 " --> pdb=" O ASP A2256 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP A2256 " --> pdb=" O PHE A2200 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A2202 " --> pdb=" O ARG A2254 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A2254 " --> pdb=" O LEU A2202 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= X, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= Y, first strand: chain 'A' and resid 2276 through 2278 Processing sheet with id= Z, first strand: chain 'A' and resid 2303 through 2305 removed outlier: 4.706A pdb=" N ILE A2317 " --> pdb=" O PHE A2305 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= AB, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.521A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 90 through 98 Processing sheet with id= AD, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.582A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.18 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7244 1.34 - 1.46: 4722 1.46 - 1.57: 10320 1.57 - 1.69: 8 1.69 - 1.81: 90 Bond restraints: 22384 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.564 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" CCF LMN A2501 " pdb=" OBX LMN A2501 " ideal model delta sigma weight residual 1.410 1.500 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.474 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 22379 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.44: 433 105.44 - 112.58: 10944 112.58 - 119.71: 7527 119.71 - 126.85: 11290 126.85 - 133.99: 196 Bond angle restraints: 30390 Sorted by residual: angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 110.25 9.97 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CCQ LMN A2501 " pdb=" OCB LMN A2501 " pdb=" CCS LMN A2501 " ideal model delta sigma weight residual 119.65 110.02 9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C SER A2050 " pdb=" N THR A2051 " pdb=" CA THR A2051 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.03e+00 angle pdb=" N GLY D 550 " pdb=" CA GLY D 550 " pdb=" C GLY D 550 " ideal model delta sigma weight residual 114.48 111.01 3.47 1.19e+00 7.06e-01 8.52e+00 angle pdb=" N VAL D 575 " pdb=" CA VAL D 575 " pdb=" C VAL D 575 " ideal model delta sigma weight residual 113.53 110.74 2.79 9.80e-01 1.04e+00 8.08e+00 ... (remaining 30385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.51: 12865 24.51 - 49.01: 436 49.01 - 73.52: 55 73.52 - 98.03: 38 98.03 - 122.53: 15 Dihedral angle restraints: 13409 sinusoidal: 5388 harmonic: 8021 Sorted by residual: dihedral pdb=" CA PHE D 544 " pdb=" C PHE D 544 " pdb=" N PRO D 545 " pdb=" CA PRO D 545 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CCC LMN A2501 " pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sinusoidal sigma weight residual 60.74 -176.73 -122.53 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 13406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2000 0.033 - 0.066: 863 0.066 - 0.099: 239 0.099 - 0.132: 189 0.132 - 0.165: 11 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CCW LMN A2501 " pdb=" CCS LMN A2501 " pdb=" CCU LMN A2501 " pdb=" OAV LMN A2501 " both_signs ideal model delta sigma weight residual False 2.30 2.45 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 3299 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 544 " 0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO D 545 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C PHE A1639 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C SER A 176 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.013 2.00e-02 2.50e+03 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 575 2.70 - 3.25: 20720 3.25 - 3.80: 35419 3.80 - 4.35: 48982 4.35 - 4.90: 80858 Nonbonded interactions: 186554 Sorted by model distance: nonbonded pdb=" OE1 GLN A 865 " pdb=" OH TYR A1006 " model vdw 2.154 2.440 nonbonded pdb=" OG SER A 231 " pdb=" OE2 GLU A 836 " model vdw 2.161 2.440 nonbonded pdb=" OD2 ASP A 539 " pdb=" OH TYR A 590 " model vdw 2.181 2.440 nonbonded pdb=" O VAL A 810 " pdb=" OG SER A 829 " model vdw 2.184 2.440 nonbonded pdb=" O LEU A2156 " pdb=" OG1 THR A2160 " model vdw 2.184 2.440 ... (remaining 186549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.250 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 64.560 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 0.161 22384 Z= 0.229 Angle : 0.557 9.973 30390 Z= 0.293 Chirality : 0.045 0.165 3302 Planarity : 0.004 0.094 4025 Dihedral : 14.056 122.534 8291 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.46 (0.16), residues: 2743 helix: -0.92 (0.30), residues: 297 sheet: 0.34 (0.16), residues: 1057 loop : -0.61 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1996 HIS 0.007 0.001 HIS B 90 PHE 0.031 0.001 PHE A 656 TYR 0.019 0.001 TYR A1679 ARG 0.007 0.000 ARG F 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 373 time to evaluate : 2.353 Fit side-chains REVERT: A 1724 TYR cc_start: 0.7491 (m-80) cc_final: 0.7210 (m-80) REVERT: B 47 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (mt0) REVERT: F 304 ILE cc_start: 0.8723 (mt) cc_final: 0.8517 (mp) outliers start: 2 outliers final: 2 residues processed: 374 average time/residue: 1.4039 time to fit residues: 596.6778 Evaluate side-chains 234 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 39 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 133 ASN A 196 GLN A 272 ASN A 401 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN A1018 ASN A1062 GLN A1302 ASN A1653 HIS A1767 GLN A1781 ASN A1955 ASN ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 22384 Z= 0.544 Angle : 0.672 9.925 30390 Z= 0.348 Chirality : 0.051 0.284 3302 Planarity : 0.005 0.094 4025 Dihedral : 9.450 102.372 3148 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 1.87 % Allowed : 8.70 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.62 (0.16), residues: 2743 helix: -1.04 (0.30), residues: 287 sheet: 0.15 (0.16), residues: 1053 loop : -0.64 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1996 HIS 0.011 0.002 HIS A2375 PHE 0.029 0.002 PHE A 656 TYR 0.019 0.002 TYR A1104 ARG 0.008 0.001 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 245 time to evaluate : 2.559 Fit side-chains REVERT: D 578 LYS cc_start: 0.7961 (tppp) cc_final: 0.7748 (mmtt) REVERT: A 1197 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 104 TYR cc_start: 0.8627 (p90) cc_final: 0.8216 (p90) REVERT: B 169 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6912 (mt-10) REVERT: F 365 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7278 (ppp) outliers start: 45 outliers final: 18 residues processed: 269 average time/residue: 1.3789 time to fit residues: 422.7019 Evaluate side-chains 245 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2331 ASN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 269 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN A1653 HIS A1767 GLN ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 209 GLN ** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22384 Z= 0.178 Angle : 0.551 7.699 30390 Z= 0.285 Chirality : 0.046 0.309 3302 Planarity : 0.004 0.079 4025 Dihedral : 7.667 83.474 3144 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.29 % Allowed : 10.00 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.49 (0.16), residues: 2743 helix: -0.85 (0.31), residues: 286 sheet: 0.22 (0.16), residues: 1062 loop : -0.56 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.020 0.001 PHE A1009 TYR 0.013 0.001 TYR A1394 ARG 0.006 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 237 time to evaluate : 2.534 Fit side-chains REVERT: A 1580 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.6770 (p-90) REVERT: B 104 TYR cc_start: 0.8554 (p90) cc_final: 0.8137 (p90) REVERT: F 365 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7263 (ppp) outliers start: 31 outliers final: 13 residues processed: 253 average time/residue: 1.4000 time to fit residues: 404.4067 Evaluate side-chains 237 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 0.0050 chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 511 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN A1485 ASN F 47 GLN F 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22384 Z= 0.487 Angle : 0.638 7.807 30390 Z= 0.333 Chirality : 0.050 0.372 3302 Planarity : 0.005 0.086 4025 Dihedral : 7.190 71.990 3144 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Rotamer: Outliers : 2.54 % Allowed : 10.25 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.64 (0.16), residues: 2743 helix: -1.07 (0.30), residues: 293 sheet: 0.10 (0.16), residues: 1052 loop : -0.60 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1996 HIS 0.005 0.002 HIS A2375 PHE 0.025 0.002 PHE A1480 TYR 0.017 0.002 TYR A1104 ARG 0.004 0.001 ARG A1643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 2.509 Fit side-chains REVERT: A 786 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7756 (pp30) REVERT: A 1197 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 1580 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.6997 (p-90) REVERT: B 104 TYR cc_start: 0.8599 (p90) cc_final: 0.8190 (p90) REVERT: F 365 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7227 (ppp) outliers start: 61 outliers final: 29 residues processed: 268 average time/residue: 1.3717 time to fit residues: 422.5610 Evaluate side-chains 254 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2331 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 0.0670 chunk 226 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 329 GLN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN A1348 ASN A1355 GLN B 94 ASN F 47 GLN F 209 GLN F 385 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22384 Z= 0.279 Angle : 0.569 8.425 30390 Z= 0.295 Chirality : 0.047 0.376 3302 Planarity : 0.004 0.080 4025 Dihedral : 6.630 74.451 3144 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.60 (0.16), residues: 2743 helix: -0.98 (0.30), residues: 293 sheet: 0.12 (0.16), residues: 1063 loop : -0.59 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.001 PHE A1009 TYR 0.013 0.001 TYR A1394 ARG 0.006 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 2.677 Fit side-chains REVERT: D 599 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7672 (ttmt) REVERT: A 786 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7730 (pp30) REVERT: A 1197 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: A 1580 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7014 (p-90) REVERT: A 1970 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 59 LYS cc_start: 0.8776 (pttm) cc_final: 0.8502 (pptt) REVERT: B 104 TYR cc_start: 0.8546 (p90) cc_final: 0.8255 (p90) REVERT: F 141 ASP cc_start: 0.7792 (p0) cc_final: 0.7556 (p0) REVERT: F 365 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7203 (ppp) outliers start: 46 outliers final: 23 residues processed: 261 average time/residue: 1.4096 time to fit residues: 420.7101 Evaluate side-chains 255 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 0.0270 chunk 238 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN A1767 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22384 Z= 0.375 Angle : 0.598 8.962 30390 Z= 0.311 Chirality : 0.048 0.386 3302 Planarity : 0.004 0.082 4025 Dihedral : 6.507 72.664 3144 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.42 % Allowed : 12.29 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.64 (0.16), residues: 2743 helix: -1.02 (0.30), residues: 293 sheet: 0.09 (0.16), residues: 1062 loop : -0.61 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.002 PHE A1009 TYR 0.015 0.001 TYR A1104 ARG 0.005 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.445 Fit side-chains REVERT: A 786 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7748 (pp30) REVERT: A 1197 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: A 1580 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.7062 (p-90) REVERT: A 1970 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 2189 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7673 (ttm170) REVERT: A 2333 GLU cc_start: 0.6774 (mp0) cc_final: 0.6574 (mp0) REVERT: B 104 TYR cc_start: 0.8608 (p90) cc_final: 0.8352 (p90) REVERT: F 365 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7220 (ppp) outliers start: 58 outliers final: 28 residues processed: 271 average time/residue: 1.3250 time to fit residues: 414.4956 Evaluate side-chains 258 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22384 Z= 0.227 Angle : 0.553 9.027 30390 Z= 0.287 Chirality : 0.046 0.371 3302 Planarity : 0.004 0.078 4025 Dihedral : 6.213 73.503 3144 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.96 % Allowed : 13.04 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.56 (0.16), residues: 2743 helix: -0.94 (0.30), residues: 293 sheet: 0.15 (0.16), residues: 1073 loop : -0.58 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.020 0.001 PHE A1009 TYR 0.013 0.001 TYR A1394 ARG 0.007 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 229 time to evaluate : 2.554 Fit side-chains REVERT: A 786 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7716 (pp30) REVERT: A 1580 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.7045 (p-90) REVERT: A 2189 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: B 59 LYS cc_start: 0.8788 (pttm) cc_final: 0.8519 (pptt) REVERT: B 104 TYR cc_start: 0.8520 (p90) cc_final: 0.8258 (p90) REVERT: F 242 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5554 (t70) REVERT: F 365 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7163 (ppp) outliers start: 47 outliers final: 27 residues processed: 262 average time/residue: 1.3995 time to fit residues: 420.4223 Evaluate side-chains 260 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22384 Z= 0.281 Angle : 0.570 9.347 30390 Z= 0.296 Chirality : 0.047 0.366 3302 Planarity : 0.004 0.077 4025 Dihedral : 6.166 72.505 3144 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.83 % Allowed : 13.24 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.55 (0.16), residues: 2743 helix: -0.83 (0.31), residues: 287 sheet: 0.14 (0.16), residues: 1075 loop : -0.58 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.001 PHE A1009 TYR 0.014 0.001 TYR B 54 ARG 0.007 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 2.551 Fit side-chains REVERT: A 786 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7728 (pp30) REVERT: A 1580 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.7072 (p-90) REVERT: A 2189 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7624 (ttm-80) REVERT: B 59 LYS cc_start: 0.8810 (pttm) cc_final: 0.8521 (pptt) REVERT: B 104 TYR cc_start: 0.8602 (p90) cc_final: 0.8397 (p90) REVERT: F 85 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8349 (mt) REVERT: F 141 ASP cc_start: 0.7782 (p0) cc_final: 0.7551 (p0) REVERT: F 242 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5618 (t70) outliers start: 44 outliers final: 30 residues processed: 261 average time/residue: 1.3780 time to fit residues: 412.4738 Evaluate side-chains 263 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1778 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1795 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 385 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22384 Z= 0.362 Angle : 0.599 9.516 30390 Z= 0.312 Chirality : 0.048 0.365 3302 Planarity : 0.004 0.079 4025 Dihedral : 6.272 71.207 3144 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.83 % Allowed : 13.62 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.65 (0.16), residues: 2743 helix: -0.97 (0.30), residues: 293 sheet: 0.08 (0.16), residues: 1072 loop : -0.64 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.022 0.002 PHE A1009 TYR 0.015 0.001 TYR A1104 ARG 0.007 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 2.374 Fit side-chains REVERT: A 786 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7744 (pp30) REVERT: A 1580 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7071 (p-90) REVERT: A 2189 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: B 59 LYS cc_start: 0.8812 (pttm) cc_final: 0.8586 (pptt) REVERT: B 104 TYR cc_start: 0.8635 (p90) cc_final: 0.8338 (p90) REVERT: F 242 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5706 (t70) outliers start: 44 outliers final: 29 residues processed: 261 average time/residue: 1.3598 time to fit residues: 408.0307 Evaluate side-chains 261 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1778 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 221 ASP Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 158 optimal weight: 0.0770 chunk 123 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN D 579 GLN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 HIS ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 385 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.003 0.047 22384 Z= 0.162 Angle : 0.544 9.639 30390 Z= 0.282 Chirality : 0.046 0.328 3302 Planarity : 0.004 0.074 4025 Dihedral : 5.946 72.300 3144 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.21 % Allowed : 14.41 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.45 (0.16), residues: 2743 helix: -0.68 (0.31), residues: 286 sheet: 0.21 (0.16), residues: 1062 loop : -0.54 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2353 HIS 0.004 0.001 HIS A1672 PHE 0.019 0.001 PHE A1804 TYR 0.013 0.001 TYR A1394 ARG 0.007 0.000 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 2.523 Fit side-chains REVERT: A 786 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7727 (pp30) REVERT: A 1580 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7087 (p-90) REVERT: A 2189 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: B 48 ARG cc_start: 0.8822 (ttt-90) cc_final: 0.8531 (ttt-90) REVERT: B 59 LYS cc_start: 0.8813 (pttm) cc_final: 0.8551 (pptt) REVERT: B 104 TYR cc_start: 0.8530 (p90) cc_final: 0.8308 (p90) REVERT: B 169 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7076 (mt-10) REVERT: F 141 ASP cc_start: 0.7728 (p0) cc_final: 0.7503 (p0) REVERT: F 242 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5527 (t70) outliers start: 29 outliers final: 20 residues processed: 256 average time/residue: 1.3987 time to fit residues: 412.0919 Evaluate side-chains 253 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 613 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 HIS A1734 ASN A1740 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN F 209 GLN F 385 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.074007 restraints weight = 35570.172| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.37 r_work: 0.2736 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22384 Z= 0.157 Angle : 0.540 9.767 30390 Z= 0.280 Chirality : 0.046 0.304 3302 Planarity : 0.004 0.072 4025 Dihedral : 5.801 72.473 3144 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.08 % Allowed : 14.70 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2743 helix: -0.67 (0.31), residues: 286 sheet: 0.25 (0.16), residues: 1061 loop : -0.50 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2353 HIS 0.004 0.001 HIS A1653 PHE 0.018 0.001 PHE A1009 TYR 0.020 0.001 TYR D 563 ARG 0.007 0.000 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7623.96 seconds wall clock time: 135 minutes 54.72 seconds (8154.72 seconds total)