Starting phenix.real_space_refine on Sat Dec 9 08:03:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/12_2023/5xwy_6777.pdb" } resolution = 3.2 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= 0.007 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: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 24 5.16 5 C 6528 2.51 5 N 1784 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A ARG 909": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9407 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 13, 'PTRANS': 10, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1086 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 33} Chain breaks: 1 Time building chain proxies: 6.38, per 1000 atoms: 0.61 Number of scatterers: 10493 At special positions: 0 Unit cell: (113.16, 111.52, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 51 15.00 O 2106 8.00 N 1784 7.00 C 6528 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: 4.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 63.7% alpha, 2.9% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 59 through 69 removed outlier: 4.058A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.524A pdb=" N TYR A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.911A pdb=" N VAL A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.945A pdb=" N LYS A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.746A pdb=" N ILE A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.707A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.993A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.838A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.551A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.590A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.522A pdb=" N TYR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.767A pdb=" N LYS A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.907A pdb=" N LYS A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 354 removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 393 removed outlier: 3.651A pdb=" N PHE A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.761A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.515A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.511A pdb=" N ALA A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.555A pdb=" N LYS A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.904A pdb=" N TYR A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.679A pdb=" N GLU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.670A pdb=" N ILE A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 4.128A pdb=" N LYS A 642 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.549A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.571A pdb=" N ILE A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.957A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.639A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.225A pdb=" N PHE A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 3.835A pdb=" N ASN A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.551A pdb=" N LYS A 839 " --> pdb=" O ASN A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 removed outlier: 4.419A pdb=" N ASN A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 883 through 895 removed outlier: 3.532A pdb=" N TYR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.530A pdb=" N LYS A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 946 removed outlier: 3.608A pdb=" N SER A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 removed outlier: 3.907A pdb=" N GLY A 966 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 4.233A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 4.246A pdb=" N VAL A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.556A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.527A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.815A pdb=" N LYS A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.750A pdb=" N LYS A1145 " --> pdb=" O CYS A1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.668A pdb=" N LYS A 165 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 160 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1104 removed outlier: 3.554A pdb=" N THR A1114 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS A1103 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A1112 " --> pdb=" O LYS A1103 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2337 1.33 - 1.45: 2437 1.45 - 1.57: 5856 1.57 - 1.68: 102 1.68 - 1.80: 45 Bond restraints: 10777 Sorted by residual: bond pdb=" CA ILE A 402 " pdb=" CB ILE A 402 " ideal model delta sigma weight residual 1.540 1.586 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.77e+00 bond pdb=" CA THR A 403 " pdb=" C THR A 403 " ideal model delta sigma weight residual 1.525 1.554 -0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" N ASN A 696 " pdb=" CA ASN A 696 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.40e+00 ... (remaining 10772 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.78: 438 106.78 - 114.75: 6302 114.75 - 122.72: 6983 122.72 - 130.69: 892 130.69 - 138.66: 55 Bond angle restraints: 14670 Sorted by residual: angle pdb=" C GLU A 544 " pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 121.70 138.66 -16.96 1.80e+00 3.09e-01 8.88e+01 angle pdb=" C MET A 44 " pdb=" N TYR A 45 " pdb=" CA TYR A 45 " ideal model delta sigma weight residual 121.70 135.33 -13.63 1.80e+00 3.09e-01 5.73e+01 angle pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 121.97 135.52 -13.55 1.80e+00 3.09e-01 5.67e+01 angle pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " ideal model delta sigma weight residual 116.35 126.09 -9.74 1.30e+00 5.92e-01 5.61e+01 angle pdb=" C GLY A 866 " pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 121.70 133.48 -11.78 1.80e+00 3.09e-01 4.28e+01 ... (remaining 14665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 6461 35.24 - 70.47: 139 70.47 - 105.71: 19 105.71 - 140.94: 3 140.94 - 176.18: 1 Dihedral angle restraints: 6623 sinusoidal: 3283 harmonic: 3340 Sorted by residual: dihedral pdb=" CA ASP A 401 " pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -54.57 -125.43 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 67.50 112.50 0 5.00e+00 4.00e-02 5.06e+02 dihedral pdb=" CA LEU A 312 " pdb=" C LEU A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 0.00 -40.28 40.28 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 6620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1545 0.124 - 0.247: 62 0.247 - 0.371: 7 0.371 - 0.494: 0 0.494 - 0.618: 1 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CB ILE A 704 " pdb=" CA ILE A 704 " pdb=" CG1 ILE A 704 " pdb=" CG2 ILE A 704 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU A 671 " pdb=" N GLU A 671 " pdb=" C GLU A 671 " pdb=" CB GLU A 671 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1612 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 677 " -0.018 2.00e-02 2.50e+03 1.77e-02 6.30e+00 pdb=" CG TYR A 677 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 677 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 677 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 677 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 677 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 677 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 677 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 202 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C GLU A 202 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 202 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 608 " -0.023 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE A 608 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 608 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 608 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 608 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 608 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 608 " -0.002 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2743 2.79 - 3.32: 9358 3.32 - 3.85: 17183 3.85 - 4.37: 21345 4.37 - 4.90: 34501 Nonbonded interactions: 85130 Sorted by model distance: nonbonded pdb=" O ILE A1120 " pdb=" OG1 THR A1133 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 178 " pdb=" OD1 ASP A 285 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 662 " pdb=" O2' A B 30 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASN A 378 " pdb=" OG SER A 780 " model vdw 2.306 2.440 nonbonded pdb=" NZ LYS A 5 " pdb=" OP2 G B 23 " model vdw 2.307 2.520 ... (remaining 85125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.260 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.790 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.008 0.080 10777 Z= 0.489 Angle : 1.175 20.001 14670 Z= 0.623 Chirality : 0.061 0.618 1615 Planarity : 0.005 0.037 1682 Dihedral : 14.310 176.181 4467 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.87 % Allowed : 6.46 % Favored : 92.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.91 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: -5.96 (0.15), residues: 1109 helix: -4.22 (0.08), residues: 692 sheet: -2.31 (0.91), residues: 30 loop : -3.12 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 971 HIS 0.016 0.003 HIS A 228 PHE 0.042 0.004 PHE A 608 TYR 0.043 0.003 TYR A 677 ARG 0.013 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 289 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 295 average time/residue: 0.3223 time to fit residues: 122.3799 Evaluate side-chains 191 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1049 time to fit residues: 2.0524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 84 ASN A 151 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 294 HIS A 314 ASN A 369 ASN A 400 ASN A 492 ASN A 547 ASN A 611 ASN A 626 ASN A 665 ASN A 771 HIS A 776 ASN A 785 GLN A 808 ASN A 908 HIS A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10777 Z= 0.180 Angle : 0.697 11.978 14670 Z= 0.375 Chirality : 0.041 0.274 1615 Planarity : 0.004 0.033 1682 Dihedral : 15.520 177.000 1933 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 2.80 % Allowed : 10.13 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.59 (0.21), residues: 1109 helix: -2.06 (0.15), residues: 720 sheet: -1.65 (1.04), residues: 25 loop : -2.77 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 971 HIS 0.009 0.002 HIS A 228 PHE 0.032 0.002 PHE A 478 TYR 0.018 0.002 TYR A 677 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 1.250 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 226 average time/residue: 0.3072 time to fit residues: 92.0584 Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1037 time to fit residues: 3.2728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 731 ASN A 828 ASN A 986 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1049 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10777 Z= 0.258 Angle : 0.692 11.563 14670 Z= 0.365 Chirality : 0.043 0.390 1615 Planarity : 0.003 0.025 1682 Dihedral : 15.384 174.867 1933 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 2.60 % Allowed : 12.73 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.24), residues: 1109 helix: -0.84 (0.18), residues: 722 sheet: -1.33 (0.95), residues: 30 loop : -2.53 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 971 HIS 0.007 0.001 HIS A 228 PHE 0.025 0.002 PHE A 478 TYR 0.026 0.002 TYR A 677 ARG 0.004 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.177 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 191 average time/residue: 0.2841 time to fit residues: 72.9589 Evaluate side-chains 168 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1043 time to fit residues: 3.7095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 369 ASN A 378 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.212 Angle : 0.646 11.244 14670 Z= 0.344 Chirality : 0.041 0.311 1615 Planarity : 0.003 0.024 1682 Dihedral : 15.295 173.906 1933 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 2.03 % Allowed : 13.69 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.44 (0.25), residues: 1109 helix: -0.19 (0.20), residues: 722 sheet: -1.14 (0.94), residues: 30 loop : -2.44 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 PHE 0.022 0.002 PHE A 848 TYR 0.019 0.001 TYR A 677 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 183 average time/residue: 0.2967 time to fit residues: 73.1790 Evaluate side-chains 167 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1480 time to fit residues: 3.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 719 GLN A 771 HIS A 930 GLN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10777 Z= 0.283 Angle : 0.688 13.823 14670 Z= 0.362 Chirality : 0.042 0.239 1615 Planarity : 0.003 0.036 1682 Dihedral : 15.289 174.446 1933 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 2.03 % Allowed : 14.85 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.18 (0.25), residues: 1109 helix: 0.03 (0.20), residues: 723 sheet: -0.95 (0.97), residues: 30 loop : -2.38 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 PHE 0.024 0.002 PHE A 848 TYR 0.022 0.002 TYR A 677 ARG 0.004 0.001 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 188 average time/residue: 0.3505 time to fit residues: 87.2404 Evaluate side-chains 171 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1186 time to fit residues: 3.9766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 378 ASN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.208 Angle : 0.659 16.987 14670 Z= 0.345 Chirality : 0.041 0.230 1615 Planarity : 0.003 0.048 1682 Dihedral : 15.186 173.422 1933 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.25 % Allowed : 16.30 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.84 (0.26), residues: 1109 helix: 0.38 (0.20), residues: 714 sheet: -0.87 (0.98), residues: 30 loop : -2.38 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.005 0.001 HIS A 228 PHE 0.019 0.002 PHE A 848 TYR 0.016 0.001 TYR A 677 ARG 0.005 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.161 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 0.3257 time to fit residues: 70.7074 Evaluate side-chains 160 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1499 time to fit residues: 3.2573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.005 0.041 10777 Z= 0.297 Angle : 0.701 14.031 14670 Z= 0.367 Chirality : 0.044 0.225 1615 Planarity : 0.003 0.045 1682 Dihedral : 15.158 174.368 1933 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.16 % Allowed : 16.10 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.92 (0.25), residues: 1109 helix: 0.27 (0.20), residues: 726 sheet: -0.80 (0.97), residues: 30 loop : -2.40 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 971 HIS 0.005 0.001 HIS A 228 PHE 0.020 0.002 PHE A 848 TYR 0.020 0.002 TYR A 677 ARG 0.008 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 174 average time/residue: 0.3295 time to fit residues: 76.3809 Evaluate side-chains 168 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1031 time to fit residues: 2.6607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.168 Angle : 0.647 20.946 14670 Z= 0.335 Chirality : 0.040 0.345 1615 Planarity : 0.002 0.028 1682 Dihedral : 14.953 172.946 1933 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.77 % Allowed : 17.16 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.57 (0.26), residues: 1109 helix: 0.63 (0.20), residues: 721 sheet: -0.59 (1.00), residues: 30 loop : -2.47 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 PHE 0.015 0.002 PHE A 848 TYR 0.014 0.001 TYR A 662 ARG 0.006 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 171 average time/residue: 0.3168 time to fit residues: 71.6416 Evaluate side-chains 155 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1095 time to fit residues: 2.3017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10777 Z= 0.176 Angle : 0.642 19.609 14670 Z= 0.334 Chirality : 0.040 0.272 1615 Planarity : 0.002 0.025 1682 Dihedral : 14.794 173.646 1933 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.39 % Allowed : 17.74 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.18 % 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: -0.40 (0.26), residues: 1109 helix: 0.75 (0.20), residues: 720 sheet: -0.48 (1.00), residues: 30 loop : -2.35 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.001 PHE A 848 TYR 0.013 0.001 TYR A 677 ARG 0.005 0.000 ARG A 978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 163 average time/residue: 0.3382 time to fit residues: 72.2311 Evaluate side-chains 154 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2071 time to fit residues: 2.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10777 Z= 0.213 Angle : 0.662 19.821 14670 Z= 0.343 Chirality : 0.041 0.257 1615 Planarity : 0.003 0.030 1682 Dihedral : 14.715 173.746 1933 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.29 % Allowed : 17.94 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.18 % 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: -0.35 (0.26), residues: 1109 helix: 0.76 (0.20), residues: 722 sheet: -0.47 (0.99), residues: 30 loop : -2.28 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.002 PHE A 848 TYR 0.016 0.001 TYR A 662 ARG 0.006 0.001 ARG A 978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 154 average time/residue: 0.3240 time to fit residues: 65.8091 Evaluate side-chains 153 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1229 time to fit residues: 2.2970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.169067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136779 restraints weight = 11296.925| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.72 r_work: 0.3040 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.179 Angle : 0.646 18.547 14670 Z= 0.335 Chirality : 0.040 0.265 1615 Planarity : 0.002 0.027 1682 Dihedral : 14.694 173.229 1933 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.10 % Allowed : 18.42 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.18 % 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: -0.28 (0.26), residues: 1109 helix: 0.87 (0.20), residues: 719 sheet: -0.42 (1.00), residues: 30 loop : -2.37 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 PHE 0.015 0.001 PHE A 848 TYR 0.014 0.001 TYR A 662 ARG 0.006 0.000 ARG A 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.06 seconds wall clock time: 46 minutes 7.63 seconds (2767.63 seconds total)