Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 18:18:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7c_18212/10_2023/8q7c_18212.pdb" } resolution = 2.9 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= 0.005 sd= 0.043 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 102 5.16 5 C 13620 2.51 5 N 3606 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 905": "OE1" <-> "OE2" Residue "B PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1366": "OE1" <-> "OE2" Residue "B TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1423": "OE1" <-> "OE2" Residue "B PHE 1584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1905": "OE1" <-> "OE2" Residue "C PHE 2265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2366": "OE1" <-> "OE2" Residue "C TYR 2615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2905": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21348 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7116 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 4, 'PTRANS': 50, 'TRANS': 835} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7116 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 4, 'PTRANS': 50, 'TRANS': 835} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7116 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 4, 'PTRANS': 50, 'TRANS': 835} Chain breaks: 5 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 10.95, per 1000 atoms: 0.51 Number of scatterers: 21348 At special positions: 0 Unit cell: (115.92, 111.78, 127.512, 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 102 16.00 O 4020 8.00 N 3606 7.00 C 13620 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: 8.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 20.1% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 4.166A pdb=" N TYR A 11 " --> pdb=" O PRO A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.571A pdb=" N TYR A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 23' Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.536A pdb=" N ALA A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 310 through 316 removed outlier: 3.588A pdb=" N GLY A 315 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 477 through 480 removed outlier: 3.771A pdb=" N LEU A 480 " --> pdb=" O ALA A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.678A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.579A pdb=" N ASP A 639 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.890A pdb=" N GLY A 752 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 774 Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.573A pdb=" N GLN A 821 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 896 removed outlier: 4.095A pdb=" N SER A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1018 through 1023 removed outlier: 3.562A pdb=" N TYR B1022 " --> pdb=" O ASP B1018 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1023' Processing helix chain 'B' and resid 1024 through 1034 removed outlier: 3.509A pdb=" N ALA B1033 " --> pdb=" O GLN B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1044 Processing helix chain 'B' and resid 1094 through 1098 Processing helix chain 'B' and resid 1310 through 1316 removed outlier: 3.535A pdb=" N GLY B1315 " --> pdb=" O GLU B1312 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B1316 " --> pdb=" O LEU B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1333 Processing helix chain 'B' and resid 1365 through 1376 Processing helix chain 'B' and resid 1383 through 1387 removed outlier: 3.752A pdb=" N TRP B1386 " --> pdb=" O PHE B1383 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 Processing helix chain 'B' and resid 1463 through 1476 Processing helix chain 'B' and resid 1477 through 1480 removed outlier: 3.871A pdb=" N LEU B1480 " --> pdb=" O ALA B1477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1477 through 1480' Processing helix chain 'B' and resid 1499 through 1506 Processing helix chain 'B' and resid 1509 through 1513 Processing helix chain 'B' and resid 1527 through 1531 removed outlier: 3.659A pdb=" N ASN B1530 " --> pdb=" O TYR B1527 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B1531 " --> pdb=" O MET B1528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1527 through 1531' Processing helix chain 'B' and resid 1539 through 1550 removed outlier: 3.654A pdb=" N LEU B1549 " --> pdb=" O ARG B1545 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B1550 " --> pdb=" O SER B1546 " (cutoff:3.500A) Processing helix chain 'B' and resid 1587 through 1591 Processing helix chain 'B' and resid 1622 through 1634 Processing helix chain 'B' and resid 1635 through 1639 removed outlier: 3.571A pdb=" N ASP B1639 " --> pdb=" O ASP B1636 " (cutoff:3.500A) Processing helix chain 'B' and resid 1685 through 1687 No H-bonds generated for 'chain 'B' and resid 1685 through 1687' Processing helix chain 'B' and resid 1704 through 1709 Processing helix chain 'B' and resid 1747 through 1754 removed outlier: 4.885A pdb=" N GLY B1752 " --> pdb=" O ASP B1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 1761 through 1774 Processing helix chain 'B' and resid 1793 through 1795 No H-bonds generated for 'chain 'B' and resid 1793 through 1795' Processing helix chain 'B' and resid 1886 through 1889 Processing helix chain 'B' and resid 1890 through 1896 removed outlier: 4.150A pdb=" N SER B1896 " --> pdb=" O LEU B1892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2008 through 2012 Processing helix chain 'C' and resid 2018 through 2023 removed outlier: 3.505A pdb=" N TYR C2022 " --> pdb=" O ASP C2018 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C2023 " --> pdb=" O ALA C2019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2018 through 2023' Processing helix chain 'C' and resid 2024 through 2034 Processing helix chain 'C' and resid 2040 through 2044 removed outlier: 3.511A pdb=" N PHE C2044 " --> pdb=" O ASN C2041 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2316 removed outlier: 3.624A pdb=" N GLN C2316 " --> pdb=" O LEU C2313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2330 through 2333 Processing helix chain 'C' and resid 2365 through 2377 Processing helix chain 'C' and resid 2383 through 2387 removed outlier: 3.719A pdb=" N TRP C2386 " --> pdb=" O PHE C2383 " (cutoff:3.500A) Processing helix chain 'C' and resid 2394 through 2399 Processing helix chain 'C' and resid 2462 through 2476 Processing helix chain 'C' and resid 2477 through 2480 removed outlier: 3.850A pdb=" N LEU C2480 " --> pdb=" O ALA C2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2477 through 2480' Processing helix chain 'C' and resid 2499 through 2506 Processing helix chain 'C' and resid 2509 through 2513 Processing helix chain 'C' and resid 2527 through 2531 removed outlier: 3.690A pdb=" N ASN C2530 " --> pdb=" O TYR C2527 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C2531 " --> pdb=" O MET C2528 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2527 through 2531' Processing helix chain 'C' and resid 2539 through 2550 removed outlier: 3.711A pdb=" N LEU C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C2550 " --> pdb=" O SER C2546 " (cutoff:3.500A) Processing helix chain 'C' and resid 2587 through 2591 Processing helix chain 'C' and resid 2622 through 2634 Processing helix chain 'C' and resid 2635 through 2639 removed outlier: 3.651A pdb=" N ASP C2639 " --> pdb=" O ASP C2636 " (cutoff:3.500A) Processing helix chain 'C' and resid 2685 through 2687 No H-bonds generated for 'chain 'C' and resid 2685 through 2687' Processing helix chain 'C' and resid 2704 through 2709 Processing helix chain 'C' and resid 2747 through 2754 removed outlier: 4.949A pdb=" N GLY C2752 " --> pdb=" O ASP C2749 " (cutoff:3.500A) Processing helix chain 'C' and resid 2761 through 2774 Processing helix chain 'C' and resid 2793 through 2795 No H-bonds generated for 'chain 'C' and resid 2793 through 2795' Processing helix chain 'C' and resid 2886 through 2889 Processing helix chain 'C' and resid 2890 through 2896 removed outlier: 4.129A pdb=" N SER C2896 " --> pdb=" O LEU C2892 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 6.990A pdb=" N ARG A 103 " --> pdb=" O ASP A 610 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 612 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP A 101 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU A 614 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 99 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 74 removed outlier: 3.935A pdb=" N ASP A 71 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 576 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 174 removed outlier: 6.701A pdb=" N ALA A 218 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR A 286 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 220 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU A 288 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 222 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 265 " --> pdb=" O VAL C2428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.617A pdb=" N GLY A 186 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 301 removed outlier: 6.475A pdb=" N GLN A 317 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 415 removed outlier: 3.708A pdb=" N ASN A 411 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C2411 " --> pdb=" O ILE C2461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 440 removed outlier: 6.268A pdb=" N GLU A 450 " --> pdb=" O GLY B1169 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA B1171 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG A 452 " --> pdb=" O ALA B1171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 440 removed outlier: 4.183A pdb=" N PHE B1265 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B1218 " --> pdb=" O VAL B1284 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR B1286 " --> pdb=" O ALA B1218 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY B1220 " --> pdb=" O TYR B1286 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU B1288 " --> pdb=" O GLY B1220 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B1222 " --> pdb=" O GLU B1288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AB4, first strand: chain 'A' and resid 648 through 655 removed outlier: 4.085A pdb=" N GLY A 676 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 661 through 669 removed outlier: 4.285A pdb=" N SER A 668 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS A 898 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 899 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 724 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 901 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE A 722 " --> pdb=" O ASP A 901 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 903 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 720 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU A 905 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 722 " --> pdb=" O TRP A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 661 through 669 removed outlier: 4.285A pdb=" N SER A 668 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS A 898 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 899 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 724 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 901 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE A 722 " --> pdb=" O ASP A 901 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 903 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 720 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU A 905 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 797 through 805 Processing sheet with id=AB8, first strand: chain 'B' and resid 1064 through 1067 removed outlier: 5.052A pdb=" N ILE B1607 " --> pdb=" O ASP B1107 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B1107 " --> pdb=" O ILE B1607 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE B1609 " --> pdb=" O VAL B1105 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B1105 " --> pdb=" O PHE B1609 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1071 through 1074 removed outlier: 3.949A pdb=" N ASP B1071 " --> pdb=" O ARG B1082 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1178 through 1179 removed outlier: 3.658A pdb=" N GLY B1186 " --> pdb=" O LYS B1193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1249 through 1250 Processing sheet with id=AC3, first strand: chain 'B' and resid 1297 through 1301 removed outlier: 6.435A pdb=" N GLN B1317 " --> pdb=" O SER B1300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1326 through 1328 Processing sheet with id=AC5, first strand: chain 'B' and resid 1423 through 1424 removed outlier: 6.247A pdb=" N GLU B1450 " --> pdb=" O GLY C2169 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA C2171 " --> pdb=" O GLU B1450 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG B1452 " --> pdb=" O ALA C2171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1439 through 1440 removed outlier: 4.236A pdb=" N PHE C2265 " --> pdb=" O VAL B1428 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA C2218 " --> pdb=" O VAL C2284 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR C2286 " --> pdb=" O ALA C2218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY C2220 " --> pdb=" O TYR C2286 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU C2288 " --> pdb=" O GLY C2220 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C2222 " --> pdb=" O GLU C2288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1640 through 1643 removed outlier: 3.593A pdb=" N GLN B1640 " --> pdb=" O VAL B1927 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1648 through 1655 removed outlier: 4.014A pdb=" N GLY B1676 " --> pdb=" O GLU B1920 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1661 through 1669 removed outlier: 4.317A pdb=" N SER B1668 " --> pdb=" O HIS B1898 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS B1898 " --> pdb=" O SER B1668 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B1899 " --> pdb=" O PHE B1724 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B1724 " --> pdb=" O ALA B1899 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP B1901 " --> pdb=" O ILE B1722 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE B1722 " --> pdb=" O ASP B1901 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B1903 " --> pdb=" O VAL B1720 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B1720 " --> pdb=" O THR B1903 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B1905 " --> pdb=" O LYS B1718 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B1722 " --> pdb=" O TRP B1730 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1661 through 1669 removed outlier: 4.317A pdb=" N SER B1668 " --> pdb=" O HIS B1898 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS B1898 " --> pdb=" O SER B1668 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B1899 " --> pdb=" O PHE B1724 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B1724 " --> pdb=" O ALA B1899 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP B1901 " --> pdb=" O ILE B1722 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE B1722 " --> pdb=" O ASP B1901 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B1903 " --> pdb=" O VAL B1720 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B1720 " --> pdb=" O THR B1903 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B1905 " --> pdb=" O LYS B1718 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1797 through 1805 Processing sheet with id=AD3, first strand: chain 'C' and resid 2064 through 2067 removed outlier: 5.107A pdb=" N ILE C2607 " --> pdb=" O ASP C2107 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP C2107 " --> pdb=" O ILE C2607 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE C2609 " --> pdb=" O VAL C2105 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C2105 " --> pdb=" O PHE C2609 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 2071 through 2074 removed outlier: 3.921A pdb=" N ASP C2071 " --> pdb=" O ARG C2082 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 2178 through 2179 removed outlier: 3.613A pdb=" N GLY C2186 " --> pdb=" O LYS C2193 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 2249 through 2250 Processing sheet with id=AD7, first strand: chain 'C' and resid 2297 through 2301 removed outlier: 6.444A pdb=" N GLN C2317 " --> pdb=" O SER C2300 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 2326 through 2328 Processing sheet with id=AD9, first strand: chain 'C' and resid 2640 through 2643 Processing sheet with id=AE1, first strand: chain 'C' and resid 2648 through 2655 removed outlier: 4.055A pdb=" N GLY C2676 " --> pdb=" O GLU C2920 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 2661 through 2669 removed outlier: 4.455A pdb=" N SER C2668 " --> pdb=" O HIS C2898 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS C2898 " --> pdb=" O SER C2668 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C2722 " --> pdb=" O TRP C2730 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 2661 through 2669 removed outlier: 4.455A pdb=" N SER C2668 " --> pdb=" O HIS C2898 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS C2898 " --> pdb=" O SER C2668 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 2797 through 2805 625 hydrogen bonds defined for protein. 1539 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: 10.84 Time building geometry restraints manager: 9.11 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: 6940 1.34 - 1.46: 5524 1.46 - 1.58: 9283 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 21930 Sorted by residual: bond pdb=" CB GLU B1905 " pdb=" CG GLU B1905 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CA LYS B1126 " pdb=" C LYS B1126 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.80e-02 3.09e+03 1.68e+00 bond pdb=" CB CYS C2758 " pdb=" SG CYS C2758 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB CYS B1758 " pdb=" SG CYS B1758 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB GLU C2905 " pdb=" CG GLU C2905 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 ... (remaining 21925 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.87: 524 104.87 - 112.16: 10394 112.16 - 119.46: 7110 119.46 - 126.75: 11490 126.75 - 134.04: 320 Bond angle restraints: 29838 Sorted by residual: angle pdb=" CB GLU B1905 " pdb=" CG GLU B1905 " pdb=" CD GLU B1905 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.70e+00 3.46e-01 1.13e+01 angle pdb=" CA ILE B1400 " pdb=" CB ILE B1400 " pdb=" CG1 ILE B1400 " ideal model delta sigma weight residual 110.40 115.90 -5.50 1.70e+00 3.46e-01 1.05e+01 angle pdb=" CB MET B1651 " pdb=" CG MET B1651 " pdb=" SD MET B1651 " ideal model delta sigma weight residual 112.70 122.18 -9.48 3.00e+00 1.11e-01 9.99e+00 angle pdb=" CB MET C2528 " pdb=" CG MET C2528 " pdb=" SD MET C2528 " ideal model delta sigma weight residual 112.70 121.90 -9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" CB MET A 651 " pdb=" CG MET A 651 " pdb=" SD MET A 651 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.35e+00 ... (remaining 29833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 11591 17.26 - 34.52: 1068 34.52 - 51.78: 240 51.78 - 69.04: 63 69.04 - 86.30: 10 Dihedral angle restraints: 12972 sinusoidal: 5142 harmonic: 7830 Sorted by residual: dihedral pdb=" CA PRO C2908 " pdb=" C PRO C2908 " pdb=" N MET C2909 " pdb=" CA MET C2909 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO B1908 " pdb=" C PRO B1908 " pdb=" N MET B1909 " pdb=" CA MET B1909 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CG ARG B1032 " pdb=" CD ARG B1032 " pdb=" NE ARG B1032 " pdb=" CZ ARG B1032 " ideal model delta sinusoidal sigma weight residual 90.00 41.17 48.83 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 12969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1972 0.032 - 0.064: 772 0.064 - 0.095: 301 0.095 - 0.127: 125 0.127 - 0.159: 4 Chirality restraints: 3174 Sorted by residual: chirality pdb=" CA ILE A 461 " pdb=" N ILE A 461 " pdb=" C ILE A 461 " pdb=" CB ILE A 461 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE C2461 " pdb=" N ILE C2461 " pdb=" C ILE C2461 " pdb=" CB ILE C2461 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CB ILE B1400 " pdb=" CA ILE B1400 " pdb=" CG1 ILE B1400 " pdb=" CG2 ILE B1400 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3171 not shown) Planarity restraints: 3906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1400 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C ILE B1400 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B1400 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B1401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B1366 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" CD GLU B1366 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU B1366 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B1366 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 366 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" CD GLU A 366 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A 366 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 366 " -0.008 2.00e-02 2.50e+03 ... (remaining 3903 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 780 2.69 - 3.24: 21152 3.24 - 3.80: 33545 3.80 - 4.35: 44515 4.35 - 4.90: 74671 Nonbonded interactions: 174663 Sorted by model distance: nonbonded pdb=" N GLU A 366 " pdb=" OE1 GLU A 366 " model vdw 2.140 2.520 nonbonded pdb=" N GLU C2366 " pdb=" OE1 GLU C2366 " model vdw 2.152 2.520 nonbonded pdb=" N GLU B1366 " pdb=" OE1 GLU B1366 " model vdw 2.176 2.520 nonbonded pdb=" N GLU C2035 " pdb=" OE1 GLU C2035 " model vdw 2.185 2.520 nonbonded pdb=" OH TYR B1773 " pdb=" OG SER B1792 " model vdw 2.209 2.440 ... (remaining 174658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.880 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 57.890 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.100 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 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 : 0.004 0.041 21930 Z= 0.286 Angle : 0.543 9.482 29838 Z= 0.282 Chirality : 0.042 0.159 3174 Planarity : 0.003 0.042 3906 Dihedral : 14.305 86.301 7962 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.64 % Allowed : 20.56 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.10 (0.17), residues: 2634 helix: 1.21 (0.32), residues: 310 sheet: 0.21 (0.24), residues: 491 loop : -0.35 (0.15), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 94 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 77 residues processed: 175 average time/residue: 1.1121 time to fit residues: 228.9997 Evaluate side-chains 169 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 92 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 77 residues processed: 0 time to fit residues: 3.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 242 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21930 Z= 0.250 Angle : 0.506 6.373 29838 Z= 0.267 Chirality : 0.043 0.182 3174 Planarity : 0.003 0.030 3906 Dihedral : 3.895 16.060 2952 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.28 % Allowed : 18.44 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.04 (0.17), residues: 2634 helix: 1.55 (0.32), residues: 303 sheet: 0.06 (0.23), residues: 530 loop : -0.30 (0.15), residues: 1801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 98 time to evaluate : 2.492 Fit side-chains outliers start: 122 outliers final: 88 residues processed: 202 average time/residue: 1.0588 time to fit residues: 255.6794 Evaluate side-chains 182 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 94 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 84 residues processed: 4 average time/residue: 1.2645 time to fit residues: 9.0290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN C2449 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21930 Z= 0.258 Angle : 0.510 8.088 29838 Z= 0.266 Chirality : 0.043 0.250 3174 Planarity : 0.003 0.030 3906 Dihedral : 3.914 19.555 2952 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.97 % Allowed : 18.27 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.65 (0.32), residues: 303 sheet: 0.06 (0.23), residues: 524 loop : -0.27 (0.15), residues: 1807 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 95 time to evaluate : 2.463 Fit side-chains outliers start: 138 outliers final: 93 residues processed: 217 average time/residue: 1.0385 time to fit residues: 271.9327 Evaluate side-chains 185 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 92 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 91 residues processed: 2 average time/residue: 1.3650 time to fit residues: 6.5251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 2.9990 chunk 182 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21930 Z= 0.222 Angle : 0.497 8.077 29838 Z= 0.257 Chirality : 0.042 0.199 3174 Planarity : 0.003 0.030 3906 Dihedral : 3.887 15.327 2952 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.84 % Allowed : 18.48 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.70 (0.32), residues: 303 sheet: 0.04 (0.23), residues: 524 loop : -0.23 (0.15), residues: 1807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 94 time to evaluate : 2.698 Fit side-chains revert: symmetry clash outliers start: 135 outliers final: 98 residues processed: 212 average time/residue: 1.0295 time to fit residues: 262.1644 Evaluate side-chains 191 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 93 time to evaluate : 2.597 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 94 residues processed: 4 average time/residue: 0.9958 time to fit residues: 8.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1774 ASN C2324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21930 Z= 0.326 Angle : 0.543 7.867 29838 Z= 0.279 Chirality : 0.043 0.260 3174 Planarity : 0.003 0.028 3906 Dihedral : 4.035 22.090 2952 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.93 % Allowed : 18.53 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.80 (0.32), residues: 303 sheet: 0.05 (0.22), residues: 558 loop : -0.21 (0.16), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 93 time to evaluate : 2.500 Fit side-chains revert: symmetry clash outliers start: 137 outliers final: 104 residues processed: 216 average time/residue: 0.9955 time to fit residues: 259.5463 Evaluate side-chains 197 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 93 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 102 residues processed: 2 average time/residue: 0.7804 time to fit residues: 5.3954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 258 optimal weight: 0.4980 chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 0.0170 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21930 Z= 0.119 Angle : 0.482 9.676 29838 Z= 0.247 Chirality : 0.042 0.225 3174 Planarity : 0.003 0.030 3906 Dihedral : 3.765 16.503 2952 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.94 % Allowed : 19.91 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.08 (0.17), residues: 2634 helix: 1.76 (0.32), residues: 303 sheet: -0.10 (0.23), residues: 508 loop : -0.15 (0.15), residues: 1823 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 96 time to evaluate : 2.408 Fit side-chains outliers start: 114 outliers final: 92 residues processed: 203 average time/residue: 1.0473 time to fit residues: 255.9270 Evaluate side-chains 185 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 93 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 91 residues processed: 1 average time/residue: 1.2731 time to fit residues: 4.9971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21930 Z= 0.364 Angle : 0.571 10.535 29838 Z= 0.290 Chirality : 0.043 0.185 3174 Planarity : 0.003 0.027 3906 Dihedral : 4.055 18.486 2952 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.15 % Allowed : 19.96 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.08 (0.17), residues: 2634 helix: 1.88 (0.33), residues: 302 sheet: -0.03 (0.22), residues: 564 loop : -0.20 (0.16), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 93 time to evaluate : 2.695 Fit side-chains outliers start: 119 outliers final: 96 residues processed: 201 average time/residue: 1.0384 time to fit residues: 251.1055 Evaluate side-chains 188 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 92 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 96 residues processed: 1 average time/residue: 1.4016 time to fit residues: 5.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21930 Z= 0.193 Angle : 0.519 11.651 29838 Z= 0.262 Chirality : 0.042 0.185 3174 Planarity : 0.003 0.028 3906 Dihedral : 3.946 17.007 2952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.06 % Allowed : 20.26 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.81 (0.32), residues: 303 sheet: -0.12 (0.23), residues: 510 loop : -0.19 (0.15), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 95 time to evaluate : 2.463 Fit side-chains outliers start: 117 outliers final: 95 residues processed: 207 average time/residue: 1.0068 time to fit residues: 250.9434 Evaluate side-chains 186 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 91 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 95 residues processed: 0 time to fit residues: 3.2136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21930 Z= 0.205 Angle : 0.538 11.984 29838 Z= 0.270 Chirality : 0.042 0.177 3174 Planarity : 0.003 0.028 3906 Dihedral : 3.921 17.096 2952 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.55 % Allowed : 21.00 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.79 (0.32), residues: 303 sheet: -0.11 (0.23), residues: 510 loop : -0.19 (0.15), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 94 time to evaluate : 2.471 Fit side-chains outliers start: 105 outliers final: 94 residues processed: 195 average time/residue: 1.0238 time to fit residues: 239.7998 Evaluate side-chains 187 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 93 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 93 residues processed: 1 average time/residue: 1.2162 time to fit residues: 4.6490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21930 Z= 0.307 Angle : 0.568 12.496 29838 Z= 0.287 Chirality : 0.043 0.195 3174 Planarity : 0.003 0.037 3906 Dihedral : 4.065 17.937 2952 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.46 % Allowed : 20.95 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.00 (0.17), residues: 2634 helix: 1.79 (0.32), residues: 303 sheet: -0.16 (0.23), residues: 510 loop : -0.22 (0.15), residues: 1821 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 93 time to evaluate : 2.827 Fit side-chains outliers start: 103 outliers final: 95 residues processed: 192 average time/residue: 1.0615 time to fit residues: 245.0694 Evaluate side-chains 187 residues out of total 2343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 92 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 94 residues processed: 1 average time/residue: 1.2732 time to fit residues: 4.8526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 64 optimal weight: 0.0000 chunk 195 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.036602 restraints weight = 80139.071| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 4.04 r_work: 0.2378 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21930 Z= 0.147 Angle : 0.539 12.808 29838 Z= 0.268 Chirality : 0.042 0.181 3174 Planarity : 0.003 0.046 3906 Dihedral : 3.880 16.671 2952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.50 % Allowed : 21.04 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2634 helix: 1.67 (0.32), residues: 303 sheet: -0.13 (0.23), residues: 509 loop : -0.16 (0.15), residues: 1822 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5209.09 seconds wall clock time: 94 minutes 56.76 seconds (5696.76 seconds total)