Starting phenix.real_space_refine on Fri Nov 17 01:07:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/11_2023/7uic_26543.pdb" } resolution = 3.7 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 72 5.16 5 C 11113 2.51 5 N 2869 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 49": "OE1" <-> "OE2" Residue "e TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 768": "OE1" <-> "OE2" Residue "e PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 1058": "OD1" <-> "OD2" Residue "o ASP 857": "OD1" <-> "OD2" Residue "o PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 971": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17303 Number of models: 1 Model: "" Number of chains: 6 Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "c" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 891 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "e" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5916 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 708} Chain breaks: 4 Chain: "n" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1780 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Chain: "o" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 894 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "p" Number of atoms: 7306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7306 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 860} Chain breaks: 3 Time building chain proxies: 9.43, per 1000 atoms: 0.54 Number of scatterers: 17303 At special positions: 0 Unit cell: (149.04, 184.92, 129.72, 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 72 16.00 O 3249 8.00 N 2869 7.00 C 11113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.98 Conformation dependent library (CDL) restraints added in 3.2 seconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 15 sheets defined 55.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'b' and resid 28 through 51 removed outlier: 3.646A pdb=" N THR b 33 " --> pdb=" O LYS b 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE b 36 " --> pdb=" O LEU b 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU b 40 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU b 45 " --> pdb=" O LYS b 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET b 46 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN b 50 " --> pdb=" O MET b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 104 Processing helix chain 'c' and resid 10 through 19 Processing helix chain 'c' and resid 20 through 22 No H-bonds generated for 'chain 'c' and resid 20 through 22' Processing helix chain 'c' and resid 23 through 56 removed outlier: 4.112A pdb=" N LEU c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Proline residue: c 42 - end of helix Processing helix chain 'c' and resid 63 through 95 Processing helix chain 'c' and resid 95 through 100 Processing helix chain 'c' and resid 100 through 110 removed outlier: 4.078A pdb=" N GLU c 104 " --> pdb=" O SER c 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 288 through 305 Processing helix chain 'e' and resid 312 through 325 removed outlier: 4.494A pdb=" N THR e 321 " --> pdb=" O TYR e 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER e 322 " --> pdb=" O SER e 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE e 325 " --> pdb=" O THR e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 356 Processing helix chain 'e' and resid 367 through 387 removed outlier: 4.555A pdb=" N LEU e 381 " --> pdb=" O ILE e 377 " (cutoff:3.500A) Proline residue: e 382 - end of helix Processing helix chain 'e' and resid 392 through 402 removed outlier: 3.847A pdb=" N VAL e 396 " --> pdb=" O SER e 392 " (cutoff:3.500A) Processing helix chain 'e' and resid 404 through 419 removed outlier: 4.448A pdb=" N VAL e 408 " --> pdb=" O ASP e 404 " (cutoff:3.500A) Processing helix chain 'e' and resid 438 through 450 removed outlier: 3.821A pdb=" N ASP e 442 " --> pdb=" O ASP e 438 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 462 removed outlier: 3.846A pdb=" N TYR e 461 " --> pdb=" O VAL e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 493 through 505 removed outlier: 3.636A pdb=" N PHE e 497 " --> pdb=" O ASN e 493 " (cutoff:3.500A) Processing helix chain 'e' and resid 506 through 510 removed outlier: 3.679A pdb=" N ILE e 510 " --> pdb=" O LEU e 507 " (cutoff:3.500A) Processing helix chain 'e' and resid 520 through 528 removed outlier: 3.503A pdb=" N GLN e 524 " --> pdb=" O ASN e 520 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS e 527 " --> pdb=" O PHE e 523 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 532 removed outlier: 3.711A pdb=" N VAL e 532 " --> pdb=" O PHE e 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 529 through 532' Processing helix chain 'e' and resid 533 through 555 removed outlier: 3.525A pdb=" N GLN e 537 " --> pdb=" O ALA e 533 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG e 538 " --> pdb=" O PRO e 534 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU e 539 " --> pdb=" O THR e 535 " (cutoff:3.500A) Processing helix chain 'e' and resid 556 through 570 removed outlier: 3.554A pdb=" N ILE e 560 " --> pdb=" O ASN e 556 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA e 561 " --> pdb=" O TYR e 557 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS e 562 " --> pdb=" O ASN e 558 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE e 569 " --> pdb=" O ALA e 565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN e 570 " --> pdb=" O LEU e 566 " (cutoff:3.500A) Processing helix chain 'e' and resid 573 through 580 removed outlier: 3.764A pdb=" N THR e 577 " --> pdb=" O HIS e 573 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE e 578 " --> pdb=" O SER e 574 " (cutoff:3.500A) Processing helix chain 'e' and resid 583 through 598 Processing helix chain 'e' and resid 599 through 604 removed outlier: 3.592A pdb=" N ARG e 602 " --> pdb=" O ARG e 599 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN e 603 " --> pdb=" O ASN e 600 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY e 604 " --> pdb=" O GLY e 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 599 through 604' Processing helix chain 'e' and resid 611 through 637 removed outlier: 3.515A pdb=" N LEU e 628 " --> pdb=" O SER e 624 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE e 630 " --> pdb=" O ALA e 626 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 648 removed outlier: 3.973A pdb=" N VAL e 644 " --> pdb=" O SER e 640 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA e 645 " --> pdb=" O VAL e 641 " (cutoff:3.500A) Processing helix chain 'e' and resid 656 through 664 removed outlier: 4.023A pdb=" N ASN e 660 " --> pdb=" O SER e 656 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER e 663 " --> pdb=" O ILE e 659 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN e 664 " --> pdb=" O ASN e 660 " (cutoff:3.500A) Processing helix chain 'e' and resid 682 through 701 removed outlier: 3.853A pdb=" N LYS e 687 " --> pdb=" O ASP e 683 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS e 689 " --> pdb=" O LEU e 685 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN e 690 " --> pdb=" O THR e 686 " (cutoff:3.500A) Processing helix chain 'e' and resid 706 through 713 removed outlier: 3.777A pdb=" N ILE e 710 " --> pdb=" O THR e 706 " (cutoff:3.500A) Processing helix chain 'e' and resid 714 through 736 removed outlier: 3.720A pdb=" N ASN e 720 " --> pdb=" O ARG e 716 " (cutoff:3.500A) Proline residue: e 723 - end of helix Processing helix chain 'e' and resid 741 through 750 removed outlier: 3.882A pdb=" N TYR e 750 " --> pdb=" O GLY e 746 " (cutoff:3.500A) Processing helix chain 'e' and resid 751 through 753 No H-bonds generated for 'chain 'e' and resid 751 through 753' Processing helix chain 'e' and resid 756 through 759 removed outlier: 3.533A pdb=" N GLY e 759 " --> pdb=" O LEU e 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 756 through 759' Processing helix chain 'e' and resid 760 through 777 removed outlier: 3.670A pdb=" N PHE e 764 " --> pdb=" O LEU e 760 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR e 765 " --> pdb=" O ILE e 761 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP e 766 " --> pdb=" O LYS e 762 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU e 767 " --> pdb=" O THR e 763 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU e 768 " --> pdb=" O PHE e 764 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN e 769 " --> pdb=" O TYR e 765 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS e 773 " --> pdb=" O GLN e 769 " (cutoff:3.500A) Processing helix chain 'e' and resid 780 through 796 removed outlier: 3.957A pdb=" N LEU e 794 " --> pdb=" O LEU e 790 " (cutoff:3.500A) Processing helix chain 'e' and resid 804 through 815 removed outlier: 3.564A pdb=" N LEU e 814 " --> pdb=" O ALA e 810 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN e 815 " --> pdb=" O VAL e 811 " (cutoff:3.500A) Processing helix chain 'e' and resid 815 through 825 removed outlier: 4.020A pdb=" N LEU e 819 " --> pdb=" O ASN e 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS e 825 " --> pdb=" O LYS e 821 " (cutoff:3.500A) Processing helix chain 'e' and resid 847 through 859 removed outlier: 3.565A pdb=" N ILE e 851 " --> pdb=" O LEU e 847 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 872 removed outlier: 3.877A pdb=" N ILE e 871 " --> pdb=" O ASP e 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN e 872 " --> pdb=" O PRO e 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 867 through 872' Processing helix chain 'e' and resid 894 through 909 removed outlier: 3.509A pdb=" N ILE e 898 " --> pdb=" O PRO e 894 " (cutoff:3.500A) Processing helix chain 'e' and resid 916 through 928 removed outlier: 3.859A pdb=" N GLU e 922 " --> pdb=" O ASP e 918 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU e 923 " --> pdb=" O TYR e 919 " (cutoff:3.500A) Processing helix chain 'e' and resid 928 through 947 removed outlier: 3.702A pdb=" N VAL e 936 " --> pdb=" O PHE e 932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS e 938 " --> pdb=" O PHE e 934 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR e 939 " --> pdb=" O ASP e 935 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU e 941 " --> pdb=" O LEU e 937 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR e 942 " --> pdb=" O LYS e 938 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS e 943 " --> pdb=" O THR e 939 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR e 946 " --> pdb=" O TYR e 942 " (cutoff:3.500A) Processing helix chain 'e' and resid 958 through 975 removed outlier: 3.786A pdb=" N VAL e 964 " --> pdb=" O ASP e 960 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE e 968 " --> pdb=" O VAL e 964 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU e 974 " --> pdb=" O TYR e 970 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR e 975 " --> pdb=" O PHE e 971 " (cutoff:3.500A) Processing helix chain 'e' and resid 980 through 992 removed outlier: 4.431A pdb=" N SER e 984 " --> pdb=" O ALA e 980 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN e 985 " --> pdb=" O GLU e 981 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU e 988 " --> pdb=" O SER e 984 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN e 992 " --> pdb=" O GLU e 988 " (cutoff:3.500A) Processing helix chain 'e' and resid 1079 through 1083 removed outlier: 4.231A pdb=" N LEU e1083 " --> pdb=" O LYS e1079 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1079 through 1083' Processing helix chain 'e' and resid 1087 through 1106 removed outlier: 3.669A pdb=" N LEU e1091 " --> pdb=" O SER e1087 " (cutoff:3.500A) Processing helix chain 'e' and resid 1109 through 1130 removed outlier: 3.734A pdb=" N TYR e1119 " --> pdb=" O LYS e1115 " (cutoff:3.500A) Processing helix chain 'n' and resid 835 through 850 Processing helix chain 'n' and resid 902 through 906 removed outlier: 4.124A pdb=" N ILE n 906 " --> pdb=" O PRO n 903 " (cutoff:3.500A) Processing helix chain 'n' and resid 907 through 914 Processing helix chain 'n' and resid 917 through 943 removed outlier: 5.146A pdb=" N SER n 930 " --> pdb=" O GLN n 926 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU n 931 " --> pdb=" O PHE n 927 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG n 942 " --> pdb=" O ILE n 938 " (cutoff:3.500A) Processing helix chain 'n' and resid 1015 through 1026 removed outlier: 4.042A pdb=" N MET n1019 " --> pdb=" O ALA n1015 " (cutoff:3.500A) Processing helix chain 'n' and resid 1058 through 1074 removed outlier: 4.578A pdb=" N GLU n1063 " --> pdb=" O PRO n1059 " (cutoff:3.500A) Proline residue: n1064 - end of helix removed outlier: 3.509A pdb=" N MET n1067 " --> pdb=" O GLU n1063 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE n1072 " --> pdb=" O GLU n1068 " (cutoff:3.500A) Processing helix chain 'o' and resid 849 through 876 removed outlier: 4.012A pdb=" N GLU o 874 " --> pdb=" O LYS o 870 " (cutoff:3.500A) Processing helix chain 'o' and resid 879 through 893 Processing helix chain 'o' and resid 906 through 915 removed outlier: 4.176A pdb=" N VAL o 910 " --> pdb=" O PRO o 906 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN o 914 " --> pdb=" O VAL o 910 " (cutoff:3.500A) Processing helix chain 'o' and resid 922 through 932 Processing helix chain 'p' and resid 272 through 277 removed outlier: 3.538A pdb=" N ASP p 277 " --> pdb=" O GLN p 273 " (cutoff:3.500A) Processing helix chain 'p' and resid 473 through 478 Processing helix chain 'p' and resid 490 through 494 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 541 through 543 No H-bonds generated for 'chain 'p' and resid 541 through 543' Processing helix chain 'p' and resid 544 through 562 removed outlier: 3.529A pdb=" N THR p 550 " --> pdb=" O SER p 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR p 556 " --> pdb=" O LEU p 552 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL p 557 " --> pdb=" O ALA p 553 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER p 559 " --> pdb=" O GLY p 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS p 561 " --> pdb=" O VAL p 557 " (cutoff:3.500A) Processing helix chain 'p' and resid 566 through 584 removed outlier: 3.551A pdb=" N THR p 570 " --> pdb=" O ALA p 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE p 571 " --> pdb=" O GLU p 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS p 576 " --> pdb=" O ALA p 572 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU p 583 " --> pdb=" O ARG p 579 " (cutoff:3.500A) Processing helix chain 'p' and resid 584 through 603 removed outlier: 3.705A pdb=" N ALA p 588 " --> pdb=" O ASP p 584 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS p 589 " --> pdb=" O ARG p 585 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU p 590 " --> pdb=" O LYS p 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR p 593 " --> pdb=" O LYS p 589 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU p 599 " --> pdb=" O LEU p 595 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR p 600 " --> pdb=" O LEU p 596 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER p 601 " --> pdb=" O LYS p 597 " (cutoff:3.500A) Processing helix chain 'p' and resid 610 through 619 removed outlier: 3.841A pdb=" N MET p 614 " --> pdb=" O PRO p 610 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP p 615 " --> pdb=" O LYS p 611 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS p 616 " --> pdb=" O GLU p 612 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR p 619 " --> pdb=" O ASP p 615 " (cutoff:3.500A) Processing helix chain 'p' and resid 622 through 634 removed outlier: 4.340A pdb=" N LEU p 628 " --> pdb=" O GLN p 624 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN p 630 " --> pdb=" O ILE p 626 " (cutoff:3.500A) Processing helix chain 'p' and resid 640 through 676 removed outlier: 4.356A pdb=" N GLU p 644 " --> pdb=" O GLU p 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA p 646 " --> pdb=" O ILE p 642 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE p 659 " --> pdb=" O VAL p 655 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG p 664 " --> pdb=" O ASN p 660 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN p 665 " --> pdb=" O GLY p 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 669 " --> pdb=" O ASN p 665 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE p 670 " --> pdb=" O PHE p 666 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU p 671 " --> pdb=" O HIS p 667 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE p 673 " --> pdb=" O ALA p 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER p 674 " --> pdb=" O ILE p 670 " (cutoff:3.500A) Processing helix chain 'p' and resid 682 through 723 removed outlier: 3.951A pdb=" N PHE p 686 " --> pdb=" O ASN p 682 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN p 687 " --> pdb=" O PRO p 683 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN p 693 " --> pdb=" O ILE p 689 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE p 696 " --> pdb=" O LYS p 692 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS p 697 " --> pdb=" O GLN p 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER p 698 " --> pdb=" O ASP p 694 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU p 699 " --> pdb=" O LEU p 695 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE p 700 " --> pdb=" O ILE p 696 " (cutoff:3.500A) Proline residue: p 701 - end of helix removed outlier: 3.715A pdb=" N TRP p 705 " --> pdb=" O PRO p 701 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE p 710 " --> pdb=" O PHE p 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR p 712 " --> pdb=" O LYS p 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU p 713 " --> pdb=" O PHE p 709 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU p 718 " --> pdb=" O THR p 714 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN p 722 " --> pdb=" O LEU p 718 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP p 723 " --> pdb=" O ILE p 719 " (cutoff:3.500A) Processing helix chain 'p' and resid 726 through 729 removed outlier: 3.669A pdb=" N TYR p 729 " --> pdb=" O ASN p 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 726 through 729' Processing helix chain 'p' and resid 730 through 738 removed outlier: 3.992A pdb=" N GLY p 734 " --> pdb=" O THR p 730 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE p 736 " --> pdb=" O VAL p 732 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 762 removed outlier: 3.702A pdb=" N ARG p 742 " --> pdb=" O ALA p 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR p 743 " --> pdb=" O LYS p 739 " (cutoff:3.500A) Processing helix chain 'p' and resid 767 through 769 No H-bonds generated for 'chain 'p' and resid 767 through 769' Processing helix chain 'p' and resid 770 through 783 removed outlier: 4.483A pdb=" N SER p 774 " --> pdb=" O LEU p 770 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU p 781 " --> pdb=" O LEU p 777 " (cutoff:3.500A) Processing helix chain 'p' and resid 787 through 809 removed outlier: 3.607A pdb=" N LEU p 795 " --> pdb=" O PHE p 791 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS p 806 " --> pdb=" O PHE p 802 " (cutoff:3.500A) Processing helix chain 'p' and resid 812 through 820 removed outlier: 3.745A pdb=" N PHE p 816 " --> pdb=" O GLN p 812 " (cutoff:3.500A) Processing helix chain 'p' and resid 825 through 827 No H-bonds generated for 'chain 'p' and resid 825 through 827' Processing helix chain 'p' and resid 828 through 843 removed outlier: 3.596A pdb=" N GLY p 832 " --> pdb=" O TYR p 828 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP p 833 " --> pdb=" O ALA p 829 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE p 834 " --> pdb=" O LYS p 830 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU p 835 " --> pdb=" O VAL p 831 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU p 836 " --> pdb=" O GLY p 832 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN p 840 " --> pdb=" O LEU p 836 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN p 841 " --> pdb=" O GLN p 837 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL p 843 " --> pdb=" O ALA p 839 " (cutoff:3.500A) Processing helix chain 'p' and resid 844 through 847 Processing helix chain 'p' and resid 848 through 855 removed outlier: 3.557A pdb=" N PHE p 854 " --> pdb=" O ALA p 850 " (cutoff:3.500A) Processing helix chain 'p' and resid 863 through 867 Processing helix chain 'p' and resid 878 through 882 Processing helix chain 'p' and resid 886 through 890 Processing helix chain 'p' and resid 891 through 895 removed outlier: 3.666A pdb=" N ARG p 895 " --> pdb=" O ILE p 892 " (cutoff:3.500A) Processing helix chain 'p' and resid 896 through 900 Processing helix chain 'p' and resid 914 through 920 Processing helix chain 'p' and resid 940 through 944 Processing helix chain 'p' and resid 954 through 960 removed outlier: 3.725A pdb=" N THR p 960 " --> pdb=" O THR p 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 479 through 482 removed outlier: 4.471A pdb=" N LEU e 479 " --> pdb=" O VAL e 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'n' and resid 856 through 860 removed outlier: 7.168A pdb=" N SER n 866 " --> pdb=" O ILE n 858 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU n 860 " --> pdb=" O GLU n 864 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU n 864 " --> pdb=" O LEU n 860 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE n 867 " --> pdb=" O CYS n 880 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR n 895 " --> pdb=" O LYS n 883 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER n 885 " --> pdb=" O ASN n 893 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN n 893 " --> pdb=" O SER n 885 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'n' and resid 956 through 963 removed outlier: 3.545A pdb=" N ASN n 958 " --> pdb=" O VAL n 970 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS n 962 " --> pdb=" O GLU n 966 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU n 966 " --> pdb=" O HIS n 962 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU n 985 " --> pdb=" O HIS n1000 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS n 987 " --> pdb=" O GLN n 998 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE n 999 " --> pdb=" O CYS n1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 938 through 939 Processing sheet with id=AA5, first strand: chain 'p' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'p' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'p' and resid 101 through 102 removed outlier: 3.538A pdb=" N PHE p 102 " --> pdb=" O GLU p 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'p' and resid 105 through 110 removed outlier: 7.145A pdb=" N CYS p 124 " --> pdb=" O SER p 106 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE p 108 " --> pdb=" O ALA p 122 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA p 122 " --> pdb=" O ILE p 108 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP p 110 " --> pdb=" O MET p 120 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET p 120 " --> pdb=" O TRP p 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET p 130 " --> pdb=" O GLN p 153 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN p 153 " --> pdb=" O MET p 130 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET p 132 " --> pdb=" O VAL p 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN p 153 " --> pdb=" O TYR p 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR p 160 " --> pdb=" O GLN p 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'p' and resid 190 through 195 removed outlier: 6.906A pdb=" N ILE p 242 " --> pdb=" O LEU p 191 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE p 193 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU p 240 " --> pdb=" O PHE p 193 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP p 195 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA p 238 " --> pdb=" O TRP p 195 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN p 253 " --> pdb=" O LYS p 236 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA p 238 " --> pdb=" O TRP p 251 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP p 251 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU p 240 " --> pdb=" O ASP p 249 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP p 249 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE p 242 " --> pdb=" O GLN p 247 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN p 247 " --> pdb=" O ILE p 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'p' and resid 216 through 224 removed outlier: 3.765A pdb=" N ARG p 220 " --> pdb=" O PHE p 207 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE p 207 " --> pdb=" O ARG p 220 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN p 222 " --> pdb=" O SER p 205 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER p 205 " --> pdb=" O GLN p 222 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL p 224 " --> pdb=" O ILE p 203 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE p 203 " --> pdb=" O VAL p 224 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS p 208 " --> pdb=" O ILE p 487 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE p 487 " --> pdb=" O CYS p 208 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS p 485 " --> pdb=" O PHE p 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 281 through 288 removed outlier: 3.966A pdb=" N PHE p 283 " --> pdb=" O TYR p 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p 301 " --> pdb=" O ASN p 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN p 306 " --> pdb=" O SER p 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR p 339 " --> pdb=" O ILE p 307 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU p 337 " --> pdb=" O PHE p 309 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS p 311 " --> pdb=" O PHE p 335 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE p 335 " --> pdb=" O LYS p 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS p 313 " --> pdb=" O ILE p 333 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE p 333 " --> pdb=" O HIS p 313 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASN p 315 " --> pdb=" O LEU p 331 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU p 331 " --> pdb=" O ASN p 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'p' and resid 353 through 358 removed outlier: 6.660A pdb=" N LEU p 353 " --> pdb=" O ASN p 377 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN p 377 " --> pdb=" O LEU p 353 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN p 355 " --> pdb=" O LEU p 375 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE p 433 " --> pdb=" O VAL p 386 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG p 388 " --> pdb=" O SER p 431 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER p 431 " --> pdb=" O ARG p 388 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG p 390 " --> pdb=" O ARG p 429 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG p 429 " --> pdb=" O ARG p 390 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA p 392 " --> pdb=" O LEU p 427 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU p 427 " --> pdb=" O ALA p 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 439 through 444 removed outlier: 6.908A pdb=" N TYR p 454 " --> pdb=" O THR p 440 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE p 442 " --> pdb=" O SER p 452 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER p 452 " --> pdb=" O ILE p 442 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER p 444 " --> pdb=" O PHE p 450 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE p 450 " --> pdb=" O SER p 444 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE p 453 " --> pdb=" O GLU p 461 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU p 461 " --> pdb=" O PHE p 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 497 through 498 removed outlier: 4.021A pdb=" N TRP p 509 " --> pdb=" O LYS p 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'p' and resid 932 through 933 788 hydrogen bonds defined for protein. 2265 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: 5.48 Time building geometry restraints manager: 7.45 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: 5031 1.34 - 1.46: 2775 1.46 - 1.58: 9727 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 17650 Sorted by residual: bond pdb=" C PRO p 504 " pdb=" N PRO p 505 " ideal model delta sigma weight residual 1.334 1.348 -0.014 1.51e-02 4.39e+03 8.51e-01 bond pdb=" C TRP p 955 " pdb=" N PRO p 956 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.61e-01 bond pdb=" CA PRO p 504 " pdb=" C PRO p 504 " ideal model delta sigma weight residual 1.517 1.525 -0.008 9.30e-03 1.16e+04 7.49e-01 bond pdb=" CD GLU b 99 " pdb=" OE1 GLU b 99 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.27e-01 bond pdb=" CA GLU b 99 " pdb=" CB GLU b 99 " ideal model delta sigma weight residual 1.528 1.542 -0.013 1.59e-02 3.96e+03 7.08e-01 ... (remaining 17645 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 419 106.45 - 113.36: 9757 113.36 - 120.26: 6313 120.26 - 127.17: 7217 127.17 - 134.07: 164 Bond angle restraints: 23870 Sorted by residual: angle pdb=" N GLN c 80 " pdb=" CA GLN c 80 " pdb=" CB GLN c 80 " ideal model delta sigma weight residual 110.39 116.35 -5.96 1.66e+00 3.63e-01 1.29e+01 angle pdb=" N GLU b 99 " pdb=" CA GLU b 99 " pdb=" CB GLU b 99 " ideal model delta sigma weight residual 110.16 115.21 -5.05 1.48e+00 4.57e-01 1.16e+01 angle pdb=" C LEU c 79 " pdb=" N GLN c 80 " pdb=" CA GLN c 80 " ideal model delta sigma weight residual 120.72 115.44 5.28 1.67e+00 3.59e-01 1.00e+01 angle pdb=" N GLU e 344 " pdb=" CA GLU e 344 " pdb=" CB GLU e 344 " ideal model delta sigma weight residual 110.28 114.05 -3.77 1.55e+00 4.16e-01 5.92e+00 angle pdb=" CA GLN c 80 " pdb=" CB GLN c 80 " pdb=" CG GLN c 80 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.70e+00 ... (remaining 23865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9639 17.23 - 34.46: 905 34.46 - 51.68: 161 51.68 - 68.91: 24 68.91 - 86.14: 13 Dihedral angle restraints: 10742 sinusoidal: 4395 harmonic: 6347 Sorted by residual: dihedral pdb=" CA GLU c 22 " pdb=" C GLU c 22 " pdb=" N ASN c 23 " pdb=" CA ASN c 23 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG ARG p 388 " pdb=" CD ARG p 388 " pdb=" NE ARG p 388 " pdb=" CZ ARG p 388 " ideal model delta sinusoidal sigma weight residual 180.00 136.18 43.82 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG e 440 " pdb=" CD ARG e 440 " pdb=" NE ARG e 440 " pdb=" CZ ARG e 440 " ideal model delta sinusoidal sigma weight residual 180.00 136.89 43.11 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 10739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1815 0.034 - 0.068: 669 0.068 - 0.101: 199 0.101 - 0.135: 54 0.135 - 0.169: 2 Chirality restraints: 2739 Sorted by residual: chirality pdb=" CA GLU e 387 " pdb=" N GLU e 387 " pdb=" C GLU e 387 " pdb=" CB GLU e 387 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA PRO n1017 " pdb=" N PRO n1017 " pdb=" C PRO n1017 " pdb=" CB PRO n1017 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA GLU b 99 " pdb=" N GLU b 99 " pdb=" C GLU b 99 " pdb=" CB GLU b 99 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2736 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP p 955 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO p 956 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO p 956 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO p 956 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR n1016 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO n1017 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO n1017 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO n1017 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO p 504 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO p 505 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO p 505 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO p 505 " 0.028 5.00e-02 4.00e+02 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1800 2.75 - 3.29: 17872 3.29 - 3.82: 27737 3.82 - 4.36: 32345 4.36 - 4.90: 53924 Nonbonded interactions: 133678 Sorted by model distance: nonbonded pdb=" OE1 GLN e 902 " pdb=" OG1 THR e 913 " model vdw 2.212 2.440 nonbonded pdb=" OG SER p 817 " pdb=" O GLU p 823 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU e 768 " pdb=" ND2 ASN e 815 " model vdw 2.236 2.520 nonbonded pdb=" OE1 GLU n 941 " pdb=" NE2 HIS n1070 " model vdw 2.239 2.520 nonbonded pdb=" OG SER p 914 " pdb=" OE1 GLU p 917 " model vdw 2.239 2.440 ... (remaining 133673 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 5.430 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 47.230 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 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 : 0.002 0.033 17650 Z= 0.136 Angle : 0.509 7.789 23870 Z= 0.254 Chirality : 0.040 0.169 2739 Planarity : 0.004 0.074 3020 Dihedral : 13.617 86.139 6592 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2108 helix: 0.77 (0.17), residues: 961 sheet: -0.35 (0.36), residues: 216 loop : 0.06 (0.20), residues: 931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2724 time to fit residues: 68.8771 Evaluate side-chains 91 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 GLN ** c 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN e 815 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 HIS ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17650 Z= 0.183 Angle : 0.606 9.160 23870 Z= 0.307 Chirality : 0.043 0.198 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.782 16.440 2269 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.81 % Allowed : 7.00 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2108 helix: 1.00 (0.16), residues: 986 sheet: -0.44 (0.34), residues: 229 loop : -0.05 (0.21), residues: 893 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.2650 time to fit residues: 45.6013 Evaluate side-chains 92 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1698 time to fit residues: 5.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 191 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17650 Z= 0.151 Angle : 0.547 13.041 23870 Z= 0.271 Chirality : 0.041 0.251 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.694 14.896 2269 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.60 % Allowed : 9.17 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2108 helix: 1.17 (0.17), residues: 987 sheet: -0.36 (0.35), residues: 229 loop : -0.08 (0.21), residues: 892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.2664 time to fit residues: 43.8685 Evaluate side-chains 89 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2290 time to fit residues: 4.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 GLN ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 488 GLN e 573 HIS ** e 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 720 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1105 ASN ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 854 ASN ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN p 687 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17650 Z= 0.330 Angle : 0.701 10.323 23870 Z= 0.364 Chirality : 0.045 0.247 2739 Planarity : 0.004 0.047 3020 Dihedral : 4.318 16.977 2269 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.36 % Allowed : 11.54 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2108 helix: 0.75 (0.16), residues: 991 sheet: -0.65 (0.33), residues: 234 loop : -0.22 (0.20), residues: 883 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 103 average time/residue: 0.2706 time to fit residues: 46.5552 Evaluate side-chains 91 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1708 time to fit residues: 7.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 776 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 641 ASN p 660 ASN p 812 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17650 Z= 0.221 Angle : 0.615 11.886 23870 Z= 0.310 Chirality : 0.042 0.216 2739 Planarity : 0.004 0.052 3020 Dihedral : 4.213 16.470 2269 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.81 % Allowed : 13.70 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2108 helix: 0.82 (0.16), residues: 1004 sheet: -0.66 (0.33), residues: 234 loop : -0.19 (0.21), residues: 870 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 97 average time/residue: 0.3002 time to fit residues: 48.2321 Evaluate side-chains 78 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1696 time to fit residues: 4.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 641 ASN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17650 Z= 0.208 Angle : 0.603 11.455 23870 Z= 0.303 Chirality : 0.042 0.175 2739 Planarity : 0.004 0.050 3020 Dihedral : 4.192 17.037 2269 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 14.56 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2108 helix: 0.83 (0.16), residues: 1014 sheet: -0.76 (0.33), residues: 252 loop : -0.10 (0.22), residues: 842 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 91 average time/residue: 0.2824 time to fit residues: 43.2796 Evaluate side-chains 81 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1704 time to fit residues: 4.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 641 ASN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17650 Z= 0.182 Angle : 0.592 10.567 23870 Z= 0.294 Chirality : 0.042 0.166 2739 Planarity : 0.003 0.051 3020 Dihedral : 4.138 18.610 2269 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 0.35 % Allowed : 15.16 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2108 helix: 0.91 (0.16), residues: 1015 sheet: -0.78 (0.32), residues: 257 loop : -0.05 (0.22), residues: 836 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 85 average time/residue: 0.2895 time to fit residues: 40.1287 Evaluate side-chains 78 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4453 time to fit residues: 4.0611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 19 optimal weight: 0.3980 chunk 160 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1120 HIS ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 465 GLN p 641 ASN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17650 Z= 0.220 Angle : 0.619 10.678 23870 Z= 0.310 Chirality : 0.043 0.304 2739 Planarity : 0.004 0.051 3020 Dihedral : 4.238 20.378 2269 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 0.60 % Allowed : 15.72 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2108 helix: 0.86 (0.16), residues: 1017 sheet: -0.93 (0.32), residues: 251 loop : -0.09 (0.22), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 88 average time/residue: 0.2808 time to fit residues: 41.1908 Evaluate side-chains 83 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1785 time to fit residues: 4.8644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17650 Z= 0.165 Angle : 0.610 15.083 23870 Z= 0.297 Chirality : 0.043 0.309 2739 Planarity : 0.004 0.054 3020 Dihedral : 4.180 21.684 2269 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 0.30 % Allowed : 16.02 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2108 helix: 0.98 (0.16), residues: 1026 sheet: -0.91 (0.32), residues: 251 loop : -0.03 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 84 average time/residue: 0.2811 time to fit residues: 39.3269 Evaluate side-chains 77 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1623 time to fit residues: 3.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17650 Z= 0.191 Angle : 0.628 16.175 23870 Z= 0.309 Chirality : 0.042 0.169 2739 Planarity : 0.004 0.058 3020 Dihedral : 4.223 22.261 2269 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 0.20 % Allowed : 16.17 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2108 helix: 1.03 (0.16), residues: 1011 sheet: -0.93 (0.32), residues: 251 loop : -0.06 (0.22), residues: 846 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 0.2900 time to fit residues: 38.7275 Evaluate side-chains 76 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1588 time to fit residues: 3.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.043565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.037064 restraints weight = 227887.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.037469 restraints weight = 182890.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.037682 restraints weight = 152920.773| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17650 Z= 0.150 Angle : 0.630 17.638 23870 Z= 0.299 Chirality : 0.042 0.172 2739 Planarity : 0.004 0.058 3020 Dihedral : 4.070 21.509 2269 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 0.20 % Allowed : 16.32 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2108 helix: 1.16 (0.16), residues: 1009 sheet: -0.86 (0.32), residues: 251 loop : -0.01 (0.22), residues: 848 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2610.65 seconds wall clock time: 50 minutes 1.58 seconds (3001.58 seconds total)