Starting phenix.real_space_refine (version: dev) on Tue Feb 28 03:02:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xfa_22168/02_2023/6xfa_22168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xfa_22168/02_2023/6xfa_22168.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/6xfa_22168/02_2023/6xfa_22168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xfa_22168/02_2023/6xfa_22168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xfa_22168/02_2023/6xfa_22168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xfa_22168/02_2023/6xfa_22168.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ASP 433": "OD1" <-> "OD2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C ASP 463": "OD1" <-> "OD2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D GLU 428": "OE1" <-> "OE2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D ASP 457": "OD1" <-> "OD2" Residue "D ASP 463": "OD1" <-> "OD2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "E ASP 433": "OD1" <-> "OD2" Residue "E ASP 457": "OD1" <-> "OD2" Residue "E ASP 463": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F ARG 137": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F ASP 457": "OD1" <-> "OD2" Residue "F ASP 463": "OD1" <-> "OD2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ASP 327": "OD1" <-> "OD2" Residue "G ARG 334": "NH1" <-> "NH2" Residue "G ARG 370": "NH1" <-> "NH2" Residue "G GLU 428": "OE1" <-> "OE2" Residue "G ASP 433": "OD1" <-> "OD2" Residue "G ASP 457": "OD1" <-> "OD2" Residue "G ASP 463": "OD1" <-> "OD2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ARG 137": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H ASP 327": "OD1" <-> "OD2" Residue "H ARG 334": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H GLU 428": "OE1" <-> "OE2" Residue "H ASP 433": "OD1" <-> "OD2" Residue "H ASP 457": "OD1" <-> "OD2" Residue "H ASP 463": "OD1" <-> "OD2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 89": "NH1" <-> "NH2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I ARG 149": "NH1" <-> "NH2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I ASP 244": "OD1" <-> "OD2" Residue "I ARG 313": "NH1" <-> "NH2" Residue "I ASP 327": "OD1" <-> "OD2" Residue "I ARG 334": "NH1" <-> "NH2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I GLU 428": "OE1" <-> "OE2" Residue "I ASP 433": "OD1" <-> "OD2" Residue "I ASP 457": "OD1" <-> "OD2" Residue "I ASP 463": "OD1" <-> "OD2" Residue "I ARG 467": "NH1" <-> "NH2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 89": "NH1" <-> "NH2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 137": "NH1" <-> "NH2" Residue "J ARG 149": "NH1" <-> "NH2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J ASP 244": "OD1" <-> "OD2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "J ASP 327": "OD1" <-> "OD2" Residue "J ARG 334": "NH1" <-> "NH2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "J GLU 428": "OE1" <-> "OE2" Residue "J ASP 433": "OD1" <-> "OD2" Residue "J ASP 457": "OD1" <-> "OD2" Residue "J ASP 463": "OD1" <-> "OD2" Residue "J ARG 467": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31730 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "B" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "C" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "D" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "E" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "F" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "G" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "H" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "I" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "J" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 400 SG CYS A 54 96.085 111.428 85.400 1.00 0.79 S ATOM 424 SG CYS A 57 95.742 113.780 82.794 1.00 0.80 S ATOM 1075 SG CYS A 138 95.274 109.880 81.114 1.00 0.71 S ATOM 1849 SG CYS A 316 111.068 88.854 85.296 1.00 0.83 S ATOM 1870 SG CYS A 319 110.130 92.188 82.780 1.00 0.84 S ATOM 2468 SG CYS A 393 108.345 89.119 83.063 1.00 0.85 S ATOM 3571 SG CYS B 54 44.607 107.589 85.424 1.00 0.79 S ATOM 3595 SG CYS B 57 42.264 107.992 82.819 1.00 0.80 S ATOM 4246 SG CYS B 138 45.828 106.343 81.136 1.00 0.71 S ATOM 5020 SG CYS B 316 70.708 114.860 85.321 1.00 0.83 S ATOM 5041 SG CYS B 319 67.246 115.001 82.805 1.00 0.84 S ATOM 5639 SG CYS B 393 69.613 112.355 83.085 1.00 0.85 S ATOM 6742 SG CYS C 54 32.349 57.474 85.424 1.00 0.79 S ATOM 6766 SG CYS C 57 31.242 55.370 82.818 1.00 0.80 S ATOM 7417 SG CYS C 138 33.911 58.250 81.136 1.00 0.71 S ATOM 8191 SG CYS C 316 33.494 84.544 85.321 1.00 0.83 S ATOM 8212 SG CYS C 319 32.291 81.295 82.805 1.00 0.84 S ATOM 8810 SG CYS C 393 35.539 82.729 83.085 1.00 0.85 S ATOM 9913 SG CYS D 54 76.224 30.321 85.422 1.00 0.79 S ATOM 9937 SG CYS D 57 77.882 28.618 82.817 1.00 0.80 S ATOM 10588 SG CYS D 138 75.968 32.046 81.134 1.00 0.71 S ATOM 11362 SG CYS D 316 50.834 39.780 85.321 1.00 0.83 S ATOM 11383 SG CYS D 319 53.552 37.631 82.805 1.00 0.84 S ATOM 11981 SG CYS D 393 53.192 41.164 83.085 1.00 0.85 S ATOM 13084 SG CYS E 54 115.590 63.667 85.424 1.00 0.79 S ATOM 13108 SG CYS E 57 117.723 64.718 82.819 1.00 0.80 S ATOM 13759 SG CYS E 138 113.871 63.958 81.136 1.00 0.71 S ATOM 14533 SG CYS E 316 98.744 42.447 85.321 1.00 0.83 S ATOM 14554 SG CYS E 319 101.628 44.367 82.805 1.00 0.84 S ATOM 15152 SG CYS E 393 98.157 45.117 83.085 1.00 0.85 S ATOM 16255 SG CYS F 54 32.354 90.714 35.417 1.00 0.79 S ATOM 16279 SG CYS F 57 31.247 92.818 38.022 1.00 0.80 S ATOM 16930 SG CYS F 138 33.916 89.938 39.704 1.00 0.71 S ATOM 17704 SG CYS F 316 33.497 63.644 35.519 1.00 0.83 S ATOM 17725 SG CYS F 319 32.294 66.893 38.035 1.00 0.84 S ATOM 18323 SG CYS F 393 35.542 65.458 37.755 1.00 0.85 S ATOM 19426 SG CYS G 54 76.234 117.859 35.413 1.00 0.79 S ATOM 19450 SG CYS G 57 77.894 119.561 38.018 1.00 0.80 S ATOM 20101 SG CYS G 138 75.978 116.134 39.701 1.00 0.71 S ATOM 20875 SG CYS G 316 50.839 108.416 35.518 1.00 0.83 S ATOM 20896 SG CYS G 319 53.558 110.564 38.033 1.00 0.84 S ATOM 21494 SG CYS G 393 53.196 107.032 37.754 1.00 0.85 S ATOM 22597 SG CYS H 54 115.586 84.532 35.416 1.00 0.79 S ATOM 22621 SG CYS H 57 117.718 83.481 38.021 1.00 0.80 S ATOM 23272 SG CYS H 138 113.866 84.241 39.703 1.00 0.71 S ATOM 24046 SG CYS H 316 98.742 105.754 35.519 1.00 0.83 S ATOM 24067 SG CYS H 319 101.625 103.834 38.035 1.00 0.84 S ATOM 24665 SG CYS H 393 98.155 103.083 37.755 1.00 0.85 S ATOM 25768 SG CYS I 54 96.047 36.761 35.419 1.00 0.79 S ATOM 25792 SG CYS I 57 95.707 34.408 38.025 1.00 0.80 S ATOM 26443 SG CYS I 138 95.240 38.307 39.707 1.00 0.71 S ATOM 27217 SG CYS I 316 111.024 59.339 35.515 1.00 0.83 S ATOM 27238 SG CYS I 319 110.089 56.003 38.032 1.00 0.84 S ATOM 27836 SG CYS I 393 108.303 59.072 37.752 1.00 0.85 S ATOM 28939 SG CYS J 54 44.587 40.614 35.416 1.00 0.79 S ATOM 28963 SG CYS J 57 42.244 40.212 38.022 1.00 0.80 S ATOM 29614 SG CYS J 138 45.809 41.859 39.704 1.00 0.71 S ATOM 30388 SG CYS J 316 70.681 33.322 35.517 1.00 0.83 S ATOM 30409 SG CYS J 319 67.220 33.184 38.033 1.00 0.84 S ATOM 31007 SG CYS J 393 69.589 35.828 37.753 1.00 0.85 S Time building chain proxies: 17.48, per 1000 atoms: 0.55 Number of scatterers: 31730 At special positions: 0 Unit cell: (147.06, 149.34, 121.98, 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) Zn 20 29.99 S 240 16.00 O 5730 8.00 N 5230 7.00 C 20510 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: 12.53 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 57 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 132 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 138 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 54 " pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 386 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 319 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 316 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 393 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 57 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 132 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 138 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 54 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 386 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 319 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 316 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 393 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 57 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 132 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 138 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 54 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 386 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 319 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 316 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 393 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 57 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 132 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 138 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 54 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 386 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 319 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 316 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 393 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 57 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 132 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 138 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 54 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 386 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 319 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 316 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 393 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 57 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 132 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 138 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 54 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 386 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 319 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 316 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 393 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 57 " pdb="ZN ZN G 500 " - pdb=" ND1 HIS G 132 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 138 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 54 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 386 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 319 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 316 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 393 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 57 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 132 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 138 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 54 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" ND1 HIS H 386 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 319 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 316 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 393 " pdb=" ZN I 500 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 57 " pdb="ZN ZN I 500 " - pdb=" ND1 HIS I 132 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 138 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 54 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" ND1 HIS I 386 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 319 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 316 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 393 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 57 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 132 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 138 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 54 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS J 386 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 319 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 316 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 393 " Number of angles added : 60 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7660 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 10 sheets defined 62.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.625A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.685A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.928A pdb=" N LEU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 147 through 167 Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.646A pdb=" N LEU B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 323 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 147 through 167 Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.591A pdb=" N LEU C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.648A pdb=" N LEU C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU C 320 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY C 323 " --> pdb=" O CYS C 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN C 376 " --> pdb=" O ARG C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.685A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU D 320 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 323 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 359 Processing helix chain 'D' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 389 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.802A pdb=" N THR D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'E' and resid 72 through 85 Processing helix chain 'E' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 147 through 167 Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 325 removed outlier: 3.532A pdb=" N GLU E 320 " --> pdb=" O CYS E 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY E 323 " --> pdb=" O CYS E 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 359 Processing helix chain 'E' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 389 Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 433 through 448 Processing helix chain 'E' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.804A pdb=" N THR E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU F 12 " --> pdb=" O THR F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 54 through 65 Processing helix chain 'F' and resid 72 through 85 Processing helix chain 'F' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 147 through 167 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU F 249 " --> pdb=" O TYR F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU F 320 " --> pdb=" O CYS F 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY F 323 " --> pdb=" O CYS F 319 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 325 " --> pdb=" O SER F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 Processing helix chain 'F' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 389 Processing helix chain 'F' and resid 390 through 400 Processing helix chain 'F' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 433 through 448 Processing helix chain 'F' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS F 460 " --> pdb=" O VAL F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 54 through 65 Processing helix chain 'G' and resid 72 through 85 Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 147 through 167 Processing helix chain 'G' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 325 removed outlier: 3.530A pdb=" N GLU G 320 " --> pdb=" O CYS G 316 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY G 323 " --> pdb=" O CYS G 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 359 Processing helix chain 'G' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN G 376 " --> pdb=" O ARG G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 389 Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU G 405 " --> pdb=" O ASN G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 423 Processing helix chain 'G' and resid 433 through 448 Processing helix chain 'G' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 482 removed outlier: 3.802A pdb=" N THR G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 72 through 85 Processing helix chain 'H' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU H 118 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 147 through 167 Processing helix chain 'H' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU H 249 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU H 300 " --> pdb=" O PRO H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU H 320 " --> pdb=" O CYS H 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY H 323 " --> pdb=" O CYS H 319 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS H 325 " --> pdb=" O SER H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 359 Processing helix chain 'H' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN H 376 " --> pdb=" O ARG H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 390 through 400 Processing helix chain 'H' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 412 No H-bonds generated for 'chain 'H' and resid 410 through 412' Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 433 through 448 Processing helix chain 'H' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS H 460 " --> pdb=" O VAL H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 482 removed outlier: 3.804A pdb=" N THR H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU I 12 " --> pdb=" O THR I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 54 through 65 Processing helix chain 'I' and resid 72 through 85 Processing helix chain 'I' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU I 118 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 134 Processing helix chain 'I' and resid 147 through 167 Processing helix chain 'I' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU I 249 " --> pdb=" O TYR I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.646A pdb=" N LEU I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU I 320 " --> pdb=" O CYS I 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY I 323 " --> pdb=" O CYS I 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS I 325 " --> pdb=" O SER I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR I 331 " --> pdb=" O ASP I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 359 Processing helix chain 'I' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN I 376 " --> pdb=" O ARG I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 389 Processing helix chain 'I' and resid 390 through 400 Processing helix chain 'I' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU I 405 " --> pdb=" O ASN I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 412 No H-bonds generated for 'chain 'I' and resid 410 through 412' Processing helix chain 'I' and resid 413 through 423 Processing helix chain 'I' and resid 433 through 448 Processing helix chain 'I' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS I 460 " --> pdb=" O VAL I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR I 479 " --> pdb=" O GLN I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU J 12 " --> pdb=" O THR J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 54 through 65 Processing helix chain 'J' and resid 72 through 85 Processing helix chain 'J' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 147 through 167 Processing helix chain 'J' and resid 245 through 252 removed outlier: 3.593A pdb=" N LEU J 249 " --> pdb=" O TYR J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU J 320 " --> pdb=" O CYS J 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 323 " --> pdb=" O CYS J 319 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS J 325 " --> pdb=" O SER J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 359 Processing helix chain 'J' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN J 376 " --> pdb=" O ARG J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 389 Processing helix chain 'J' and resid 390 through 400 Processing helix chain 'J' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 412 No H-bonds generated for 'chain 'J' and resid 410 through 412' Processing helix chain 'J' and resid 413 through 423 Processing helix chain 'J' and resid 433 through 448 Processing helix chain 'J' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS J 460 " --> pdb=" O VAL J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR J 479 " --> pdb=" O GLN J 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA3, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'E' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 309 Processing sheet with id=AA7, first strand: chain 'G' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'H' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'I' and resid 308 through 309 Processing sheet with id=AB1, first strand: chain 'J' and resid 308 through 309 1530 hydrogen bonds defined for protein. 4500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.79 Time building geometry restraints manager: 13.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10070 1.34 - 1.46: 7348 1.46 - 1.58: 14772 1.58 - 1.70: 0 1.70 - 1.81: 320 Bond restraints: 32510 Sorted by residual: bond pdb=" CB TRP E 91 " pdb=" CG TRP E 91 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP B 91 " pdb=" CG TRP B 91 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.05e+00 bond pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 bond pdb=" CB TRP C 91 " pdb=" CG TRP C 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 bond pdb=" CB TRP G 91 " pdb=" CG TRP G 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 ... (remaining 32505 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.17: 1265 107.17 - 113.88: 18560 113.88 - 120.60: 13496 120.60 - 127.31: 10538 127.31 - 134.03: 401 Bond angle restraints: 44260 Sorted by residual: angle pdb=" CA CYS E 136 " pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " ideal model delta sigma weight residual 114.40 119.93 -5.53 2.30e+00 1.89e-01 5.79e+00 angle pdb=" CA CYS C 136 " pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " ideal model delta sigma weight residual 114.40 119.91 -5.51 2.30e+00 1.89e-01 5.73e+00 angle pdb=" CA CYS F 136 " pdb=" CB CYS F 136 " pdb=" SG CYS F 136 " ideal model delta sigma weight residual 114.40 119.90 -5.50 2.30e+00 1.89e-01 5.72e+00 angle pdb=" CA CYS B 136 " pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " ideal model delta sigma weight residual 114.40 119.89 -5.49 2.30e+00 1.89e-01 5.70e+00 angle pdb=" CA CYS D 136 " pdb=" CB CYS D 136 " pdb=" SG CYS D 136 " ideal model delta sigma weight residual 114.40 119.88 -5.48 2.30e+00 1.89e-01 5.68e+00 ... (remaining 44255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 17047 16.78 - 33.56: 1846 33.56 - 50.33: 367 50.33 - 67.11: 30 67.11 - 83.89: 40 Dihedral angle restraints: 19330 sinusoidal: 7490 harmonic: 11840 Sorted by residual: dihedral pdb=" CA CYS G 389 " pdb=" C CYS G 389 " pdb=" N ASP G 390 " pdb=" CA ASP G 390 " ideal model delta harmonic sigma weight residual -180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 dihedral pdb=" CA CYS A 389 " pdb=" C CYS A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta harmonic sigma weight residual -180.00 -164.66 -15.34 0 5.00e+00 4.00e-02 9.41e+00 dihedral pdb=" CA CYS I 389 " pdb=" C CYS I 389 " pdb=" N ASP I 390 " pdb=" CA ASP I 390 " ideal model delta harmonic sigma weight residual -180.00 -164.69 -15.31 0 5.00e+00 4.00e-02 9.37e+00 ... (remaining 19327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2413 0.028 - 0.057: 1683 0.057 - 0.085: 656 0.085 - 0.114: 241 0.114 - 0.142: 87 Chirality restraints: 5080 Sorted by residual: chirality pdb=" CA ASP J 68 " pdb=" N ASP J 68 " pdb=" C ASP J 68 " pdb=" CB ASP J 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ASP D 68 " pdb=" N ASP D 68 " pdb=" C ASP D 68 " pdb=" CB ASP D 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASP G 68 " pdb=" N ASP G 68 " pdb=" C ASP G 68 " pdb=" CB ASP G 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 5077 not shown) Planarity restraints: 5620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 38 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 39 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 39 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 38 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO D 39 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.026 5.00e-02 4.00e+02 ... (remaining 5617 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4269 2.74 - 3.28: 31028 3.28 - 3.82: 49304 3.82 - 4.36: 57958 4.36 - 4.90: 100777 Nonbonded interactions: 243336 Sorted by model distance: nonbonded pdb=" OG1 THR J 359 " pdb=" OE1 GLN J 360 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR C 359 " pdb=" OE1 GLN C 360 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR H 359 " pdb=" OE1 GLN H 360 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR D 359 " pdb=" OE1 GLN D 360 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR I 359 " pdb=" OE1 GLN I 360 " model vdw 2.205 2.440 ... (remaining 243331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 20 6.06 5 S 240 5.16 5 C 20510 2.51 5 N 5230 2.21 5 O 5730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.500 Check model and map are aligned: 0.430 Process input model: 84.310 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.300 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 0.040 32510 Z= 0.366 Angle : 0.663 7.669 44260 Z= 0.355 Chirality : 0.045 0.142 5080 Planarity : 0.005 0.048 5620 Dihedral : 14.344 83.890 11670 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.11), residues: 4000 helix: -1.43 (0.10), residues: 2320 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 492 time to evaluate : 3.588 Fit side-chains outliers start: 20 outliers final: 0 residues processed: 502 average time/residue: 0.4355 time to fit residues: 349.1440 Evaluate side-chains 387 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 3.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 8.9990 chunk 303 optimal weight: 0.0970 chunk 168 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 233 optimal weight: 0.8980 chunk 363 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN B 15 GLN B 65 ASN C 15 GLN C 150 ASN D 15 GLN D 65 ASN D 150 ASN E 150 ASN F 15 GLN F 150 ASN G 15 GLN G 150 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 15 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN J 150 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 32510 Z= 0.159 Angle : 0.560 10.661 44260 Z= 0.283 Chirality : 0.041 0.293 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.517 18.625 4330 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 4000 helix: -0.11 (0.11), residues: 2330 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 439 time to evaluate : 4.001 Fit side-chains outliers start: 38 outliers final: 28 residues processed: 458 average time/residue: 0.4521 time to fit residues: 336.0356 Evaluate side-chains 409 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 381 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2946 time to fit residues: 20.4604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 363 optimal weight: 0.9990 chunk 393 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN D 15 GLN ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN J 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 32510 Z= 0.233 Angle : 0.592 12.329 44260 Z= 0.291 Chirality : 0.042 0.133 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.455 23.166 4330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4000 helix: 0.20 (0.11), residues: 2390 sheet: None (None), residues: 0 loop : -2.81 (0.14), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 377 time to evaluate : 4.105 Fit side-chains outliers start: 38 outliers final: 29 residues processed: 407 average time/residue: 0.4312 time to fit residues: 283.6421 Evaluate side-chains 373 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 344 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2694 time to fit residues: 19.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 365 optimal weight: 3.9990 chunk 386 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN E 65 ASN G 15 GLN G 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 32510 Z= 0.224 Angle : 0.573 11.719 44260 Z= 0.283 Chirality : 0.041 0.132 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.351 20.799 4330 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4000 helix: 0.42 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.63 (0.14), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 372 time to evaluate : 3.851 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 397 average time/residue: 0.4426 time to fit residues: 288.5370 Evaluate side-chains 367 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 346 time to evaluate : 3.578 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2847 time to fit residues: 16.0634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 267 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 32510 Z= 0.250 Angle : 0.589 11.683 44260 Z= 0.289 Chirality : 0.041 0.134 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.386 21.357 4330 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4000 helix: 0.47 (0.11), residues: 2450 sheet: None (None), residues: 0 loop : -2.64 (0.15), residues: 1550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 358 time to evaluate : 3.683 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 384 average time/residue: 0.4116 time to fit residues: 260.6535 Evaluate side-chains 366 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 344 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2819 time to fit residues: 16.8253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.6980 chunk 348 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 387 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 203 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN C 65 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN D 15 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN G 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 32510 Z= 0.146 Angle : 0.535 11.701 44260 Z= 0.262 Chirality : 0.039 0.136 5080 Planarity : 0.004 0.054 5620 Dihedral : 4.102 19.033 4330 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4000 helix: 0.91 (0.11), residues: 2340 sheet: None (None), residues: 0 loop : -2.36 (0.14), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 406 time to evaluate : 4.061 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 418 average time/residue: 0.3997 time to fit residues: 279.7661 Evaluate side-chains 376 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 366 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2780 time to fit residues: 10.2671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 220 optimal weight: 0.0570 chunk 282 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 385 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 32510 Z= 0.135 Angle : 0.525 11.708 44260 Z= 0.255 Chirality : 0.039 0.149 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.930 19.742 4330 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 4000 helix: 1.23 (0.11), residues: 2320 sheet: None (None), residues: 0 loop : -2.20 (0.14), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 421 time to evaluate : 3.981 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 427 average time/residue: 0.3955 time to fit residues: 284.9187 Evaluate side-chains 390 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 385 time to evaluate : 4.085 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2816 time to fit residues: 7.9936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 2.9990 chunk 153 optimal weight: 0.0370 chunk 230 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 262 optimal weight: 0.0370 chunk 190 optimal weight: 4.9990 chunk 35 optimal weight: 0.0020 chunk 303 optimal weight: 4.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 GLN F 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 32510 Z= 0.123 Angle : 0.531 11.702 44260 Z= 0.252 Chirality : 0.038 0.144 5080 Planarity : 0.004 0.054 5620 Dihedral : 3.763 19.318 4330 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 4000 helix: 1.46 (0.11), residues: 2310 sheet: None (None), residues: 0 loop : -2.05 (0.15), residues: 1690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 431 time to evaluate : 3.762 Fit side-chains outliers start: 26 outliers final: 20 residues processed: 443 average time/residue: 0.3722 time to fit residues: 284.1789 Evaluate side-chains 418 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 398 time to evaluate : 3.794 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2988 time to fit residues: 16.4538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 1.9990 chunk 369 optimal weight: 0.8980 chunk 336 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 324 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 32510 Z= 0.157 Angle : 0.560 12.014 44260 Z= 0.263 Chirality : 0.039 0.140 5080 Planarity : 0.004 0.054 5620 Dihedral : 3.838 20.735 4330 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 4000 helix: 1.38 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -2.00 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 384 time to evaluate : 3.842 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 390 average time/residue: 0.3880 time to fit residues: 261.0023 Evaluate side-chains 374 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 370 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3029 time to fit residues: 7.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 0.4980 chunk 379 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 chunk 180 optimal weight: 0.4980 chunk 264 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 366 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 245 optimal weight: 0.0070 chunk 194 optimal weight: 7.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 32510 Z= 0.122 Angle : 0.551 12.463 44260 Z= 0.256 Chirality : 0.038 0.142 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.696 18.884 4330 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 4000 helix: 1.58 (0.11), residues: 2360 sheet: None (None), residues: 0 loop : -1.99 (0.15), residues: 1640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 415 time to evaluate : 3.824 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 415 average time/residue: 0.3734 time to fit residues: 268.8261 Evaluate side-chains 391 residues out of total 3510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 388 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2774 time to fit residues: 6.5720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 317 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 326 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 GLN F 446 GLN G 15 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.104021 restraints weight = 40285.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105672 restraints weight = 32203.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106751 restraints weight = 27498.173| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 32510 Z= 0.274 Angle : 0.626 12.644 44260 Z= 0.299 Chirality : 0.042 0.139 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.160 21.703 4330 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 4000 helix: 1.32 (0.11), residues: 2370 sheet: None (None), residues: 0 loop : -2.05 (0.15), residues: 1630 =============================================================================== Job complete usr+sys time: 5691.26 seconds wall clock time: 105 minutes 59.24 seconds (6359.24 seconds total)