Starting phenix.real_space_refine on Mon Mar 11 04:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/03_2024/6mg8_9111_updated.pdb" } resolution = 3.6 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= 0.003 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 29 5.16 5 C 4653 2.51 5 N 1165 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 946": "NH1" <-> "NH2" Residue "A TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7034 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7034 Unusual residues: {'CLR': 4} Classifications: {'peptide': 985, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 266} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 940, None: 4} Not linked: pdbres="CYS A1167 " pdbres="CLR A1401 " Not linked: pdbres="CLR A1401 " pdbres="CLR A1402 " Not linked: pdbres="CLR A1402 " pdbres="CLR A1403 " Not linked: pdbres="CLR A1403 " pdbres="CLR A1404 " Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 881 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 7, 'GLU:plan': 33, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 483 Time building chain proxies: 4.32, per 1000 atoms: 0.61 Number of scatterers: 7034 At special positions: 0 Unit cell: (83.84, 110.04, 121.83, 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 29 16.00 O 1187 8.00 N 1165 7.00 C 4653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.04 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: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 3 sheets defined 53.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.753A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 103 removed outlier: 3.903A pdb=" N PHE A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.694A pdb=" N THR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 247 through 257 removed outlier: 4.093A pdb=" N GLU A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.642A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.813A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.609A pdb=" N LEU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 removed outlier: 3.674A pdb=" N GLY A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TRP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 removed outlier: 3.949A pdb=" N ALA A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.605A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.827A pdb=" N GLU A 525 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N CYS A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 529 " --> pdb=" O CYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.562A pdb=" N SER A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 588 removed outlier: 4.338A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 3.636A pdb=" N ASP A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.915A pdb=" N ALA A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 733 through 756 removed outlier: 3.648A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A 756 " --> pdb=" O TYR A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.908A pdb=" N PHE A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 removed outlier: 4.118A pdb=" N PHE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 850 removed outlier: 4.152A pdb=" N ASP A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 873 Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 906 through 909 No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 918 through 923 removed outlier: 4.036A pdb=" N SER A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 3.807A pdb=" N ILE A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1006 through 1033 removed outlier: 4.562A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1092 removed outlier: 3.750A pdb=" N GLY A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1108 removed outlier: 4.257A pdb=" N ALA A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1122 Processing helix chain 'A' and resid 1125 through 1128 Processing helix chain 'A' and resid 1132 through 1137 Processing helix chain 'A' and resid 1139 through 1154 Processing helix chain 'A' and resid 1156 through 1163 Processing sheet with id= A, first strand: chain 'A' and resid 346 through 352 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.630A pdb=" N VAL A 176 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 178 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 181 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 959 through 964 327 hydrogen bonds defined for protein. 954 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: 2.22 Time building geometry restraints manager: 3.07 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: 2223 1.34 - 1.46: 1789 1.46 - 1.58: 3161 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 7221 Sorted by residual: bond pdb=" C10 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C10 CLR A1403 " pdb=" C5 CLR A1403 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C10 CLR A1402 " pdb=" C5 CLR A1402 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C10 CLR A1404 " pdb=" C5 CLR A1404 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C4 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.506 1.397 0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.41: 116 103.41 - 111.07: 2950 111.07 - 118.73: 2776 118.73 - 126.39: 3985 126.39 - 134.05: 130 Bond angle restraints: 9957 Sorted by residual: angle pdb=" C HIS A 930 " pdb=" N ARG A 931 " pdb=" CA ARG A 931 " ideal model delta sigma weight residual 120.97 131.75 -10.78 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C GLU A 108 " pdb=" N THR A 109 " pdb=" CA THR A 109 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" N GLY A 862 " pdb=" CA GLY A 862 " pdb=" C GLY A 862 " ideal model delta sigma weight residual 111.78 116.20 -4.42 1.69e+00 3.50e-01 6.83e+00 angle pdb=" C ASP A 895 " pdb=" N ALA A 896 " pdb=" CA ALA A 896 " ideal model delta sigma weight residual 122.15 115.01 7.14 2.83e+00 1.25e-01 6.37e+00 angle pdb=" N ASP A 895 " pdb=" CA ASP A 895 " pdb=" C ASP A 895 " ideal model delta sigma weight residual 110.80 116.17 -5.37 2.13e+00 2.20e-01 6.37e+00 ... (remaining 9952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 3945 16.65 - 33.29: 303 33.29 - 49.94: 74 49.94 - 66.58: 4 66.58 - 83.23: 5 Dihedral angle restraints: 4331 sinusoidal: 1463 harmonic: 2868 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA VAL A 894 " pdb=" C VAL A 894 " pdb=" N ASP A 895 " pdb=" CA ASP A 895 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LYS A 191 " pdb=" C LYS A 191 " pdb=" N SER A 192 " pdb=" CA SER A 192 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1168 0.106 - 0.211: 26 0.211 - 0.317: 6 0.317 - 0.423: 3 0.423 - 0.529: 7 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C10 CLR A1401 " pdb=" C1 CLR A1401 " pdb=" C5 CLR A1401 " pdb=" C9 CLR A1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C10 CLR A1404 " pdb=" C1 CLR A1404 " pdb=" C5 CLR A1404 " pdb=" C9 CLR A1404 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C10 CLR A1402 " pdb=" C1 CLR A1402 " pdb=" C5 CLR A1402 " pdb=" C9 CLR A1402 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1207 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1067 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A1068 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1068 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1068 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 931 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 932 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 354 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 355 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.019 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 157 2.71 - 3.25: 7584 3.25 - 3.80: 11083 3.80 - 4.35: 13614 4.35 - 4.90: 22479 Nonbonded interactions: 54917 Sorted by model distance: nonbonded pdb=" NH2 ARG A 280 " pdb=" O GLY A 315 " model vdw 2.157 2.520 nonbonded pdb=" O PRO A 856 " pdb=" OH TYR A 870 " model vdw 2.229 2.440 nonbonded pdb=" O TRP A1013 " pdb=" OG SER A1017 " model vdw 2.280 2.440 nonbonded pdb=" OG1 THR A 485 " pdb=" OE1 GLN A 562 " model vdw 2.299 2.440 nonbonded pdb=" O THR A 411 " pdb=" N ASP A 415 " model vdw 2.304 2.520 ... (remaining 54912 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 7.200 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.200 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.006 0.117 7221 Z= 0.405 Angle : 0.747 10.778 9957 Z= 0.362 Chirality : 0.061 0.529 1210 Planarity : 0.004 0.040 1242 Dihedral : 12.860 83.230 2476 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.49 (0.23), residues: 981 helix: -1.83 (0.18), residues: 562 sheet: -4.46 (0.49), residues: 47 loop : -2.59 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 830 HIS 0.003 0.001 HIS A 175 PHE 0.015 0.001 PHE A 502 TYR 0.015 0.001 TYR A 999 ARG 0.002 0.000 ARG A 931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9230 (mp) cc_final: 0.8790 (tt) REVERT: A 358 MET cc_start: 0.9062 (tpt) cc_final: 0.8782 (tpp) REVERT: A 489 LEU cc_start: 0.8479 (tp) cc_final: 0.8277 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1223 time to fit residues: 21.8508 Evaluate side-chains 84 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 182 GLN A 228 GLN A 314 GLN A 506 HIS A 809 HIS A 875 GLN A 915 ASN A 926 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7221 Z= 0.239 Angle : 0.598 7.941 9957 Z= 0.294 Chirality : 0.041 0.149 1210 Planarity : 0.004 0.039 1242 Dihedral : 6.311 44.512 1302 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.93 % Allowed : 17.16 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.02 (0.26), residues: 981 helix: -0.60 (0.21), residues: 563 sheet: -3.86 (0.58), residues: 46 loop : -2.04 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 849 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.002 PHE A 781 TYR 0.013 0.001 TYR A 999 ARG 0.001 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.828 Fit side-chains REVERT: A 248 LEU cc_start: 0.9169 (mp) cc_final: 0.8758 (tt) REVERT: A 1002 LEU cc_start: 0.9148 (mt) cc_final: 0.8912 (mt) REVERT: A 1056 MET cc_start: 0.9046 (mmm) cc_final: 0.8834 (mmm) REVERT: A 1091 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8527 (pt) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.1177 time to fit residues: 19.5680 Evaluate side-chains 97 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7221 Z= 0.243 Angle : 0.602 10.123 9957 Z= 0.294 Chirality : 0.041 0.161 1210 Planarity : 0.004 0.038 1242 Dihedral : 6.104 56.592 1302 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.45 % Allowed : 19.61 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.32 (0.27), residues: 981 helix: 0.03 (0.22), residues: 559 sheet: -3.64 (0.59), residues: 46 loop : -1.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 830 HIS 0.003 0.001 HIS A 344 PHE 0.013 0.002 PHE A 569 TYR 0.014 0.001 TYR A 999 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 569 PHE cc_start: 0.8922 (m-80) cc_final: 0.8555 (m-10) REVERT: A 1002 LEU cc_start: 0.9157 (mt) cc_final: 0.8923 (mt) REVERT: A 1091 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8561 (pt) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.1127 time to fit residues: 20.1227 Evaluate side-chains 101 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.0020 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7221 Z= 0.182 Angle : 0.569 9.568 9957 Z= 0.276 Chirality : 0.040 0.139 1210 Planarity : 0.003 0.035 1242 Dihedral : 5.788 59.406 1302 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.50 % Allowed : 20.32 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.82 (0.28), residues: 981 helix: 0.45 (0.22), residues: 561 sheet: -3.41 (0.62), residues: 45 loop : -1.65 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 837 HIS 0.002 0.001 HIS A 175 PHE 0.022 0.001 PHE A 781 TYR 0.022 0.001 TYR A 438 ARG 0.001 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: A 414 ASP cc_start: 0.7964 (t0) cc_final: 0.7729 (t0) REVERT: A 561 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 569 PHE cc_start: 0.8823 (m-80) cc_final: 0.8470 (m-10) REVERT: A 1002 LEU cc_start: 0.9123 (mt) cc_final: 0.8745 (mt) REVERT: A 1056 MET cc_start: 0.8928 (mmm) cc_final: 0.8615 (mmm) REVERT: A 1091 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8612 (pt) outliers start: 20 outliers final: 10 residues processed: 123 average time/residue: 0.1272 time to fit residues: 23.8572 Evaluate side-chains 107 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0030 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7221 Z= 0.211 Angle : 0.615 10.781 9957 Z= 0.292 Chirality : 0.041 0.288 1210 Planarity : 0.004 0.035 1242 Dihedral : 5.667 58.583 1302 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.03 % Allowed : 21.89 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.28), residues: 981 helix: 0.61 (0.22), residues: 564 sheet: -3.37 (0.60), residues: 45 loop : -1.61 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 344 PHE 0.012 0.001 PHE A1090 TYR 0.031 0.001 TYR A 999 ARG 0.005 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: A 561 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 569 PHE cc_start: 0.8832 (m-80) cc_final: 0.8490 (m-10) REVERT: A 819 MET cc_start: 0.8389 (ttm) cc_final: 0.8071 (ttp) REVERT: A 1002 LEU cc_start: 0.9161 (mt) cc_final: 0.8828 (mt) REVERT: A 1091 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8579 (pt) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.1120 time to fit residues: 20.0332 Evaluate side-chains 106 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 936 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7221 Z= 0.186 Angle : 0.591 10.731 9957 Z= 0.280 Chirality : 0.040 0.198 1210 Planarity : 0.003 0.036 1242 Dihedral : 5.594 56.790 1302 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.55 % Allowed : 21.89 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.28), residues: 981 helix: 0.81 (0.23), residues: 563 sheet: -3.15 (0.65), residues: 45 loop : -1.57 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 PHE 0.024 0.001 PHE A 781 TYR 0.031 0.001 TYR A 999 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: A 561 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 569 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8385 (m-10) REVERT: A 819 MET cc_start: 0.8363 (ttm) cc_final: 0.8038 (ttp) REVERT: A 1002 LEU cc_start: 0.9122 (mt) cc_final: 0.8805 (mt) REVERT: A 1006 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: A 1019 SER cc_start: 0.9506 (t) cc_final: 0.9223 (m) REVERT: A 1056 MET cc_start: 0.8943 (mmm) cc_final: 0.8650 (mmm) REVERT: A 1091 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8577 (pt) REVERT: A 1125 MET cc_start: 0.8284 (tpp) cc_final: 0.7917 (tpp) outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 0.1134 time to fit residues: 20.9601 Evaluate side-chains 109 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7221 Z= 0.193 Angle : 0.590 10.941 9957 Z= 0.280 Chirality : 0.041 0.184 1210 Planarity : 0.003 0.035 1242 Dihedral : 5.574 56.457 1302 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.73 % Allowed : 22.94 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.28), residues: 981 helix: 0.88 (0.23), residues: 564 sheet: -3.04 (0.67), residues: 45 loop : -1.48 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 344 PHE 0.014 0.001 PHE A1090 TYR 0.028 0.001 TYR A 999 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7583 (pp30) REVERT: A 561 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9053 (mm) REVERT: A 569 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (m-10) REVERT: A 819 MET cc_start: 0.8353 (ttm) cc_final: 0.8028 (ttp) REVERT: A 906 TYR cc_start: 0.8713 (m-80) cc_final: 0.8311 (m-10) REVERT: A 1002 LEU cc_start: 0.9111 (mt) cc_final: 0.8796 (mt) REVERT: A 1006 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: A 1019 SER cc_start: 0.9518 (t) cc_final: 0.9250 (m) REVERT: A 1049 MET cc_start: 0.8619 (ttp) cc_final: 0.8178 (ttm) REVERT: A 1056 MET cc_start: 0.8949 (mmm) cc_final: 0.8664 (mmm) REVERT: A 1091 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8628 (pt) REVERT: A 1125 MET cc_start: 0.8369 (tpp) cc_final: 0.7918 (tpp) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.1099 time to fit residues: 18.8997 Evaluate side-chains 110 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7221 Z= 0.250 Angle : 0.627 11.785 9957 Z= 0.297 Chirality : 0.042 0.198 1210 Planarity : 0.003 0.035 1242 Dihedral : 5.625 56.091 1302 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.90 % Allowed : 23.82 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.31 (0.28), residues: 981 helix: 0.90 (0.23), residues: 564 sheet: -3.08 (0.67), residues: 45 loop : -1.52 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 837 HIS 0.004 0.001 HIS A 344 PHE 0.026 0.001 PHE A 781 TYR 0.027 0.001 TYR A 999 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7688 (pp30) REVERT: A 561 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9078 (mm) REVERT: A 569 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8413 (m-10) REVERT: A 819 MET cc_start: 0.8359 (ttm) cc_final: 0.8029 (ttp) REVERT: A 1002 LEU cc_start: 0.9120 (mt) cc_final: 0.8812 (mt) REVERT: A 1006 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: A 1019 SER cc_start: 0.9495 (t) cc_final: 0.9201 (m) REVERT: A 1049 MET cc_start: 0.8666 (ttp) cc_final: 0.8230 (ttm) REVERT: A 1056 MET cc_start: 0.8964 (mmm) cc_final: 0.8630 (mmm) REVERT: A 1091 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8552 (pt) REVERT: A 1125 MET cc_start: 0.8436 (tpp) cc_final: 0.7909 (tpp) outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.1114 time to fit residues: 19.4763 Evaluate side-chains 113 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7221 Z= 0.289 Angle : 0.651 12.034 9957 Z= 0.309 Chirality : 0.043 0.226 1210 Planarity : 0.004 0.037 1242 Dihedral : 5.794 56.244 1302 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.73 % Allowed : 23.82 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.31 (0.28), residues: 981 helix: 0.89 (0.23), residues: 565 sheet: -3.16 (0.67), residues: 45 loop : -1.51 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 837 HIS 0.004 0.001 HIS A 344 PHE 0.009 0.001 PHE A 834 TYR 0.025 0.001 TYR A 999 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 325 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: A 561 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9088 (mm) REVERT: A 569 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: A 819 MET cc_start: 0.8347 (ttm) cc_final: 0.8012 (ttp) REVERT: A 1002 LEU cc_start: 0.9164 (mt) cc_final: 0.8839 (mt) REVERT: A 1019 SER cc_start: 0.9510 (t) cc_final: 0.9220 (m) REVERT: A 1049 MET cc_start: 0.8679 (ttp) cc_final: 0.8240 (ttm) REVERT: A 1056 MET cc_start: 0.8979 (mmm) cc_final: 0.8727 (mmm) REVERT: A 1091 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8608 (pt) REVERT: A 1125 MET cc_start: 0.8458 (tpp) cc_final: 0.7919 (tpp) outliers start: 27 outliers final: 22 residues processed: 112 average time/residue: 0.1374 time to fit residues: 24.2888 Evaluate side-chains 112 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7221 Z= 0.199 Angle : 0.625 12.851 9957 Z= 0.291 Chirality : 0.042 0.288 1210 Planarity : 0.003 0.035 1242 Dihedral : 5.669 58.455 1302 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.73 % Allowed : 23.99 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.17 (0.28), residues: 981 helix: 1.03 (0.23), residues: 556 sheet: -2.99 (0.69), residues: 45 loop : -1.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 830 HIS 0.003 0.001 HIS A 275 PHE 0.025 0.001 PHE A 781 TYR 0.027 0.001 TYR A 999 ARG 0.002 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7627 (pp30) REVERT: A 325 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: A 569 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8411 (m-10) REVERT: A 819 MET cc_start: 0.8326 (ttm) cc_final: 0.7992 (ttp) REVERT: A 1002 LEU cc_start: 0.9100 (mt) cc_final: 0.8784 (mt) REVERT: A 1006 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: A 1019 SER cc_start: 0.9511 (t) cc_final: 0.9231 (m) REVERT: A 1049 MET cc_start: 0.8654 (ttp) cc_final: 0.8213 (ttm) REVERT: A 1056 MET cc_start: 0.8857 (mmm) cc_final: 0.8570 (mmm) REVERT: A 1091 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8559 (pt) REVERT: A 1125 MET cc_start: 0.8440 (tpp) cc_final: 0.7898 (tpp) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.1143 time to fit residues: 19.8439 Evaluate side-chains 109 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091702 restraints weight = 14257.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092510 restraints weight = 7237.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093532 restraints weight = 5239.641| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.004 0.033 7221 Z= 0.265 Angle : 0.651 12.881 9957 Z= 0.305 Chirality : 0.043 0.292 1210 Planarity : 0.004 0.036 1242 Dihedral : 5.772 59.114 1302 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.20 % Allowed : 24.52 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.20 (0.28), residues: 981 helix: 0.98 (0.23), residues: 562 sheet: -3.02 (0.68), residues: 45 loop : -1.45 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 837 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.001 PHE A 743 TYR 0.025 0.001 TYR A 999 ARG 0.002 0.000 ARG A 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.12 seconds wall clock time: 29 minutes 53.58 seconds (1793.58 seconds total)