Starting phenix.real_space_refine on Sat Feb 24 12:40:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvs_12611/02_2024/7nvs_12611.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.983 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 97 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 27521 2.51 5 N 7749 2.21 5 O 8446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 146": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 50": "OE1" <-> "OE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ASP 83": "OD1" <-> "OD2" Residue "W PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W ASP 146": "OD1" <-> "OD2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W GLU 165": "OE1" <-> "OE2" Residue "W ASP 172": "OD1" <-> "OD2" Residue "W GLU 182": "OE1" <-> "OE2" Residue "W ARG 192": "NH1" <-> "NH2" Residue "W ASP 196": "OD1" <-> "OD2" Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 93": "OD1" <-> "OD2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ASP 110": "OD1" <-> "OD2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 147": "OD1" <-> "OD2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 213": "OD1" <-> "OD2" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44073 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1015 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 991 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 98.166 109.141 65.442 1.00 36.59 S ATOM 486 SG CYS A 74 98.322 106.733 62.483 1.00 32.93 S ATOM 533 SG CYS A 81 97.116 105.659 65.968 1.00 32.64 S ATOM 768 SG CYS A 111 139.703 84.440 71.079 1.00 41.00 S ATOM 796 SG CYS A 114 140.380 85.182 67.577 1.00 39.75 S ATOM 1109 SG CYS A 154 141.683 81.961 69.042 1.00 43.42 S ATOM 1132 SG CYS A 184 143.176 85.300 70.104 1.00 43.18 S ATOM 19919 SG CYS B1119 108.255 98.089 53.780 1.00 30.25 S ATOM 19941 SG CYS B1122 109.764 97.316 57.180 1.00 31.60 S ATOM 20056 SG CYS B1137 108.382 100.763 56.517 1.00 34.76 S ATOM 20077 SG CYS B1140 111.595 99.393 54.859 1.00 38.31 S ATOM 21044 SG CYS C 88 33.175 100.180 74.559 1.00 18.87 S ATOM 21057 SG CYS C 90 35.927 102.069 76.668 1.00 26.31 S ATOM 21092 SG CYS C 94 32.382 101.838 77.640 1.00 15.72 S ATOM 21114 SG CYS C 97 34.650 98.877 77.700 1.00 10.58 S ATOM 28400 SG CYS I 17 126.553 40.816 129.107 1.00 33.14 S ATOM 28424 SG CYS I 20 126.480 44.421 128.005 1.00 33.49 S ATOM 28585 SG CYS I 39 127.607 41.774 125.639 1.00 34.19 S ATOM 28610 SG CYS I 42 129.698 42.819 128.869 1.00 34.83 S ATOM 28962 SG CYS I 86 86.245 22.618 125.283 1.00 26.52 S ATOM 28986 SG CYS I 89 84.186 22.883 128.439 1.00 31.10 S ATOM 29190 SG CYS I 114 84.331 25.742 126.139 1.00 21.10 S ATOM 29225 SG CYS I 119 87.316 24.762 128.202 1.00 31.99 S ATOM 29336 SG CYS J 7 41.531 71.544 91.749 1.00 18.97 S ATOM 29360 SG CYS J 10 38.474 71.270 89.607 1.00 7.95 S ATOM 29624 SG CYS J 44 40.427 68.169 90.633 1.00 5.14 S ATOM 29630 SG CYS J 45 38.239 70.070 92.851 1.00 1.13 S ATOM 30750 SG CYS L 19 62.051 103.685 113.305 1.00 14.72 S ATOM 30769 SG CYS L 22 59.170 105.057 115.274 1.00 18.98 S ATOM 30886 SG CYS L 36 61.919 107.334 114.227 1.00 16.67 S ATOM 30912 SG CYS L 39 62.420 104.051 117.254 1.00 22.10 S ATOM 31094 SG CYS M 15 77.323 113.848 60.849 1.00 31.21 S ATOM 31241 SG CYS M 34 74.681 113.553 63.654 1.00 28.75 S ATOM 31263 SG CYS M 37 74.016 111.785 59.528 1.00 29.82 S ATOM 42122 SG CYS W 129 108.001 126.965 63.563 1.00 43.06 S ATOM 42142 SG CYS W 132 108.654 123.538 65.073 1.00 45.33 S ATOM 42314 SG CYS W 154 106.706 123.899 61.793 1.00 46.26 S ATOM 42338 SG CYS W 157 105.157 124.978 65.143 1.00 44.19 S Time building chain proxies: 24.08, per 1000 atoms: 0.55 Number of scatterers: 44073 At special positions: 0 Unit cell: (176.4, 170.1, 183.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 249 16.00 P 97 15.00 Mg 1 11.99 O 8446 8.00 N 7749 7.00 C 27521 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: 19.22 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " Number of angles added : 54 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9910 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 0 sheets defined 36.3% alpha, 0.0% beta 44 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 13.71 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.613A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.773A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.518A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.533A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.568A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.008A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.518A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 683 removed outlier: 8.135A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.642A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.626A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.381A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1187 through 1196 removed outlier: 4.104A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.577A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.571A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.573A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.476A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.679A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.529A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.773A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.790A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.291A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.888A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.636A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.502A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.536A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 removed outlier: 3.866A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.893A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.540A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.521A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.819A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.691A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.859A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 128 removed outlier: 3.533A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 183 removed outlier: 3.682A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'M' and resid 226 through 241 Processing helix chain 'M' and resid 250 through 263 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 6 through 9 Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 165 removed outlier: 3.852A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.277A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 14 Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.898A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 122 through 136 removed outlier: 3.944A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 192 removed outlier: 3.893A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.549A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.398A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.557A pdb=" N LYS U 43 " --> pdb=" O MET U 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 45 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 329 No H-bonds generated for 'chain 'U' and resid 326 through 329' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.799A pdb=" N GLY W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 removed outlier: 3.648A pdb=" N ILE W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.907A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG W 119 " --> pdb=" O GLU W 115 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN W 123 " --> pdb=" O ARG W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 removed outlier: 3.799A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 183 removed outlier: 4.098A pdb=" N MET W 168 " --> pdb=" O GLU W 165 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.677A pdb=" N ALA W 178 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG W 179 " --> pdb=" O LEU W 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN W 183 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 194 Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.503A pdb=" N GLN X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG X 91 " --> pdb=" O THR X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.766A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 removed outlier: 3.727A pdb=" N GLN X 117 " --> pdb=" O LEU X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 removed outlier: 3.583A pdb=" N ALA X 174 " --> pdb=" O ASP X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 188 removed outlier: 6.009A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 4.109A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3051 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 16.32 Time building geometry restraints manager: 20.52 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: 14383 1.34 - 1.46: 9657 1.46 - 1.58: 20458 1.58 - 1.70: 193 1.70 - 1.83: 392 Bond restraints: 45083 Sorted by residual: bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CZ ARG A 483 " pdb=" NH2 ARG A 483 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.03e+00 ... (remaining 45078 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.10: 1472 106.10 - 113.08: 24661 113.08 - 120.06: 15397 120.06 - 127.04: 19100 127.04 - 134.02: 651 Bond angle restraints: 61281 Sorted by residual: angle pdb=" N VAL B 353 " pdb=" CA VAL B 353 " pdb=" C VAL B 353 " ideal model delta sigma weight residual 113.20 109.71 3.49 9.60e-01 1.09e+00 1.32e+01 angle pdb=" CA TRP B 453 " pdb=" CB TRP B 453 " pdb=" CG TRP B 453 " ideal model delta sigma weight residual 113.60 108.36 5.24 1.90e+00 2.77e-01 7.60e+00 angle pdb=" C ASP H 71 " pdb=" N ASP H 72 " pdb=" CA ASP H 72 " ideal model delta sigma weight residual 125.66 130.70 -5.04 1.85e+00 2.92e-01 7.42e+00 angle pdb=" N GLN A 539 " pdb=" CA GLN A 539 " pdb=" C GLN A 539 " ideal model delta sigma weight residual 110.80 116.58 -5.78 2.13e+00 2.20e-01 7.38e+00 angle pdb=" N GLU I 105 " pdb=" CA GLU I 105 " pdb=" CB GLU I 105 " ideal model delta sigma weight residual 114.17 111.26 2.91 1.14e+00 7.69e-01 6.54e+00 ... (remaining 61276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24228 17.97 - 35.95: 2387 35.95 - 53.92: 564 53.92 - 71.89: 155 71.89 - 89.86: 47 Dihedral angle restraints: 27381 sinusoidal: 12083 harmonic: 15298 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA TRP B 453 " pdb=" C TRP B 453 " pdb=" N GLY B 454 " pdb=" CA GLY B 454 " ideal model delta harmonic sigma weight residual 180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 27378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4872 0.033 - 0.067: 1237 0.067 - 0.100: 439 0.100 - 0.133: 282 0.133 - 0.167: 6 Chirality restraints: 6836 Sorted by residual: chirality pdb=" CA PRO A 478 " pdb=" N PRO A 478 " pdb=" C PRO A 478 " pdb=" CB PRO A 478 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE B 152 " pdb=" N ILE B 152 " pdb=" C ILE B 152 " pdb=" CB ILE B 152 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 6833 not shown) Planarity restraints: 7603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO O 298 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1379 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CD GLU A1379 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A1379 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A1379 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 396 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.022 5.00e-02 4.00e+02 ... (remaining 7600 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 366 2.55 - 3.14: 35614 3.14 - 3.72: 72456 3.72 - 4.31: 104434 4.31 - 4.90: 168291 Nonbonded interactions: 381161 Sorted by model distance: nonbonded pdb=" OH TYR B 814 " pdb=" OE1 GLU B 900 " model vdw 1.961 2.440 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 1.977 2.440 nonbonded pdb=" OE1 GLU A 893 " pdb=" OG SER E 197 " model vdw 1.989 2.440 nonbonded pdb=" OG SER A1147 " pdb=" OD2 ASP A1351 " model vdw 2.045 2.440 nonbonded pdb=" OH TYR A 875 " pdb=" OE2 GLU F 61 " model vdw 2.075 2.440 ... (remaining 381156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.310 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: 0.040 Extract box with map and model: 20.610 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 131.950 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 0.003 0.044 45083 Z= 0.189 Angle : 0.459 6.820 61281 Z= 0.265 Chirality : 0.040 0.167 6836 Planarity : 0.003 0.066 7603 Dihedral : 15.533 89.862 17471 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 1.40 (0.12), residues: 5187 helix: 1.94 (0.12), residues: 1908 sheet: 0.79 (0.18), residues: 864 loop : 0.24 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 453 HIS 0.006 0.001 HIS M 18 PHE 0.018 0.001 PHE C 63 TYR 0.015 0.001 TYR B1048 ARG 0.014 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 926 time to evaluate : 5.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 MET cc_start: 0.8904 (mmm) cc_final: 0.8471 (mmt) REVERT: A 1231 ILE cc_start: 0.7803 (mt) cc_final: 0.7399 (mt) REVERT: A 1451 MET cc_start: 0.8394 (mmm) cc_final: 0.8180 (mmm) REVERT: C 61 ASP cc_start: 0.7982 (m-30) cc_final: 0.7771 (m-30) REVERT: C 89 THR cc_start: 0.8545 (p) cc_final: 0.8270 (p) REVERT: I 111 TYR cc_start: 0.8363 (m-80) cc_final: 0.8034 (m-80) REVERT: K 22 ASN cc_start: 0.7958 (m-40) cc_final: 0.7624 (m-40) REVERT: M 35 PRO cc_start: 0.5794 (Cg_endo) cc_final: 0.5591 (Cg_exo) REVERT: U 51 MET cc_start: 0.2977 (mmp) cc_final: 0.2021 (mpp) outliers start: 0 outliers final: 1 residues processed: 926 average time/residue: 1.8055 time to fit residues: 2017.9883 Evaluate side-chains 667 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 666 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 440 optimal weight: 6.9990 chunk 395 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 135 optimal weight: 0.0010 chunk 266 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 409 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 474 optimal weight: 7.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 372 ASN A 465 HIS A 671 ASN A 757 GLN A 804 HIS B 52 GLN B 503 ASN B 537 GLN B 741 HIS B 913 GLN B 968 ASN B1115 GLN C 51 GLN C 217 GLN I 46 GLN I 91 HIS J 52 HIS L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 140 ASN M 263 GLN M 287 GLN ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN R 194 HIS R 208 GLN W 109 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 45083 Z= 0.314 Angle : 0.584 11.253 61281 Z= 0.302 Chirality : 0.044 0.279 6836 Planarity : 0.004 0.056 7603 Dihedral : 12.673 114.670 6792 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.43 % Allowed : 10.63 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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 (0.12), residues: 5187 helix: 1.47 (0.12), residues: 1946 sheet: 0.69 (0.18), residues: 849 loop : 0.13 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 453 HIS 0.009 0.001 HIS M 18 PHE 0.024 0.002 PHE G 44 TYR 0.021 0.002 TYR G 3 ARG 0.008 0.001 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 675 time to evaluate : 5.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7462 (mmtp) REVERT: A 266 MET cc_start: 0.4054 (ppp) cc_final: 0.3471 (pmt) REVERT: A 310 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6513 (tp) REVERT: A 410 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: A 660 MET cc_start: 0.8766 (mmm) cc_final: 0.8470 (mmt) REVERT: A 1411 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8049 (mt) REVERT: B 358 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: B 764 MET cc_start: 0.8622 (mtt) cc_final: 0.8162 (mtp) REVERT: B 897 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.4612 (mpt-90) REVERT: B 918 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8528 (p90) REVERT: C 89 THR cc_start: 0.8457 (p) cc_final: 0.8206 (p) REVERT: C 210 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: E 23 ASP cc_start: 0.8220 (m-30) cc_final: 0.7971 (m-30) REVERT: I 25 TYR cc_start: 0.7369 (m-80) cc_final: 0.7113 (m-80) REVERT: K 22 ASN cc_start: 0.7927 (m-40) cc_final: 0.7649 (m-40) REVERT: M 44 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7315 (mtt180) REVERT: M 311 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6087 (p0) REVERT: Q 115 LYS cc_start: 0.6193 (ttpt) cc_final: 0.5976 (tttt) REVERT: R 160 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7396 (tp40) REVERT: U 51 MET cc_start: 0.3141 (mmp) cc_final: 0.2068 (mpp) REVERT: W 76 MET cc_start: 0.2313 (mmp) cc_final: 0.2025 (mmm) outliers start: 113 outliers final: 29 residues processed: 730 average time/residue: 1.6892 time to fit residues: 1506.4140 Evaluate side-chains 639 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 600 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 394 optimal weight: 0.7980 chunk 322 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 474 optimal weight: 20.0000 chunk 513 optimal weight: 40.0000 chunk 422 optimal weight: 8.9990 chunk 470 optimal weight: 40.0000 chunk 161 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS A 731 ASN A 905 ASN A1093 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 145 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS B1115 GLN C 217 GLN J 26 GLN ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 GLN R 208 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 45083 Z= 0.338 Angle : 0.574 12.245 61281 Z= 0.297 Chirality : 0.044 0.249 6836 Planarity : 0.004 0.065 7603 Dihedral : 12.726 75.176 6790 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.08 % Allowed : 12.35 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.79 (0.12), residues: 5187 helix: 1.21 (0.12), residues: 1949 sheet: 0.66 (0.18), residues: 851 loop : 0.00 (0.13), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 453 HIS 0.012 0.001 HIS M 18 PHE 0.030 0.002 PHE G 77 TYR 0.025 0.002 TYR G 3 ARG 0.010 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 627 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 266 MET cc_start: 0.4182 (ppp) cc_final: 0.3584 (pmt) REVERT: A 410 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7740 (m-40) REVERT: A 660 MET cc_start: 0.8835 (mmm) cc_final: 0.8524 (mmt) REVERT: A 762 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: A 845 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 1071 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: B 111 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8407 (t0) REVERT: B 255 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7787 (ptt-90) REVERT: B 358 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6682 (pt0) REVERT: B 579 ASP cc_start: 0.7394 (t0) cc_final: 0.7169 (t0) REVERT: B 764 MET cc_start: 0.8654 (mtm) cc_final: 0.8174 (mtp) REVERT: B 897 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.4606 (mpt-90) REVERT: B 918 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8563 (p90) REVERT: C 89 THR cc_start: 0.8419 (p) cc_final: 0.8154 (p) REVERT: C 91 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6286 (mm-30) REVERT: C 210 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: I 25 TYR cc_start: 0.7256 (m-80) cc_final: 0.6998 (m-80) REVERT: K 22 ASN cc_start: 0.7948 (m-40) cc_final: 0.7694 (m-40) REVERT: K 97 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: L 27 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6374 (tt0) REVERT: M 44 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7375 (mtt180) REVERT: M 271 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: M 277 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (mm) REVERT: M 311 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.6054 (p0) REVERT: Q 115 LYS cc_start: 0.6120 (ttpt) cc_final: 0.5851 (tttt) REVERT: Q 169 LYS cc_start: 0.2572 (tppt) cc_final: 0.2204 (mmmt) REVERT: U 51 MET cc_start: 0.3269 (mmp) cc_final: 0.2132 (mpp) REVERT: U 358 MET cc_start: 0.3814 (tmm) cc_final: 0.2686 (mmt) outliers start: 143 outliers final: 54 residues processed: 702 average time/residue: 1.6931 time to fit residues: 1453.9940 Evaluate side-chains 667 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 598 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 271 GLN Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 469 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 476 optimal weight: 6.9990 chunk 504 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 451 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 673 GLN A 731 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1129 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 98 HIS B 649 ASN B1030 ASN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 217 GLN H 76 ASN M 263 GLN M 271 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN R 152 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 45083 Z= 0.543 Angle : 0.671 17.905 61281 Z= 0.343 Chirality : 0.048 0.263 6836 Planarity : 0.005 0.081 7603 Dihedral : 12.879 76.998 6790 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.83 % Allowed : 13.75 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.12), residues: 5187 helix: 0.85 (0.12), residues: 1954 sheet: 0.45 (0.18), residues: 852 loop : -0.17 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 453 HIS 0.015 0.002 HIS M 18 PHE 0.025 0.002 PHE B 918 TYR 0.023 0.002 TYR B1048 ARG 0.015 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 622 time to evaluate : 5.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7600 (mmtt) REVERT: A 266 MET cc_start: 0.4216 (ppp) cc_final: 0.3713 (pmt) REVERT: A 357 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8107 (ptpt) REVERT: A 410 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7854 (m-40) REVERT: A 613 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: A 660 MET cc_start: 0.8869 (mmm) cc_final: 0.8613 (mmt) REVERT: A 845 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 1015 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 1071 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: A 1306 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7446 (ttmm) REVERT: B 111 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 388 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 897 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.4749 (mpt-90) REVERT: B 918 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8691 (p90) REVERT: B 1109 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: C 89 THR cc_start: 0.8461 (p) cc_final: 0.8213 (p) REVERT: C 91 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6253 (mm-30) REVERT: C 210 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: I 45 GLN cc_start: 0.7418 (mt0) cc_final: 0.7157 (mt0) REVERT: K 22 ASN cc_start: 0.8037 (m-40) cc_final: 0.7781 (m-40) REVERT: K 97 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: L 27 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: L 58 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7330 (mmm-85) REVERT: M 44 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7459 (mtt180) REVERT: M 311 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5988 (p0) REVERT: Q 115 LYS cc_start: 0.6194 (ttpt) cc_final: 0.5982 (tttt) REVERT: U 51 MET cc_start: 0.3293 (mmp) cc_final: 0.1960 (mpp) outliers start: 178 outliers final: 87 residues processed: 724 average time/residue: 1.6792 time to fit residues: 1484.8929 Evaluate side-chains 702 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 596 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 202 MET Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 420 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 375 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 430 optimal weight: 20.0000 chunk 348 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 452 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN H 76 ASN M 263 GLN ** U 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 45083 Z= 0.414 Angle : 0.614 12.857 61281 Z= 0.314 Chirality : 0.045 0.240 6836 Planarity : 0.005 0.064 7603 Dihedral : 12.866 77.788 6790 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.85 % Allowed : 15.15 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.37 (0.12), residues: 5187 helix: 0.86 (0.12), residues: 1955 sheet: 0.38 (0.18), residues: 833 loop : -0.22 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 453 HIS 0.014 0.001 HIS M 18 PHE 0.021 0.002 PHE B 918 TYR 0.022 0.002 TYR I 54 ARG 0.012 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 602 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7580 (mmtt) REVERT: A 266 MET cc_start: 0.4338 (OUTLIER) cc_final: 0.3715 (pmt) REVERT: A 410 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: A 613 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 660 MET cc_start: 0.8855 (mmm) cc_final: 0.8580 (mmt) REVERT: A 1015 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 1035 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: A 1071 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: A 1184 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.6360 (t) REVERT: A 1224 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6606 (mtt180) REVERT: A 1306 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7439 (ttmm) REVERT: A 1379 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: B 111 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 388 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8112 (t80) REVERT: B 918 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8698 (p90) REVERT: C 89 THR cc_start: 0.8441 (p) cc_final: 0.8182 (p) REVERT: C 91 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6264 (mm-30) REVERT: C 210 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: K 22 ASN cc_start: 0.8058 (m-40) cc_final: 0.7803 (m-40) REVERT: K 97 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: L 58 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7235 (mmm-85) REVERT: M 36 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5626 (pt0) REVERT: M 44 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7490 (mtt180) REVERT: U 51 MET cc_start: 0.3378 (mmp) cc_final: 0.2007 (mpp) outliers start: 179 outliers final: 94 residues processed: 704 average time/residue: 1.7037 time to fit residues: 1465.4298 Evaluate side-chains 695 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 581 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 202 MET Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 169 optimal weight: 2.9990 chunk 454 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 505 optimal weight: 0.0670 chunk 419 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 145 GLN B1030 ASN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN C 217 GLN H 76 ASN M 271 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45083 Z= 0.187 Angle : 0.538 12.608 61281 Z= 0.275 Chirality : 0.041 0.208 6836 Planarity : 0.004 0.053 7603 Dihedral : 12.752 77.704 6790 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.76 % Allowed : 17.13 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.59 (0.12), residues: 5187 helix: 1.12 (0.12), residues: 1948 sheet: 0.48 (0.18), residues: 828 loop : -0.14 (0.13), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 453 HIS 0.015 0.001 HIS M 18 PHE 0.018 0.001 PHE K 13 TYR 0.024 0.001 TYR I 54 ARG 0.012 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 615 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.4407 (ppp) cc_final: 0.3776 (pmt) REVERT: A 410 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7515 (m-40) REVERT: A 660 MET cc_start: 0.8724 (mmm) cc_final: 0.8485 (mmt) REVERT: A 695 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: A 1015 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 1071 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 1224 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6536 (mtt180) REVERT: B 111 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8350 (t0) REVERT: B 358 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6661 (pt0) REVERT: B 388 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8028 (t80) REVERT: B 578 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7873 (mmtt) REVERT: B 673 VAL cc_start: 0.8906 (t) cc_final: 0.8695 (m) REVERT: C 89 THR cc_start: 0.8347 (p) cc_final: 0.8096 (p) REVERT: C 210 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: K 22 ASN cc_start: 0.8024 (m-40) cc_final: 0.7730 (m-40) REVERT: M 44 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7273 (mtt180) REVERT: M 277 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8303 (mm) REVERT: U 51 MET cc_start: 0.3439 (mmp) cc_final: 0.2041 (mpp) outliers start: 128 outliers final: 50 residues processed: 686 average time/residue: 1.6613 time to fit residues: 1395.0254 Evaluate side-chains 640 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 579 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 486 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 368 optimal weight: 0.0980 chunk 285 optimal weight: 20.0000 chunk 425 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 503 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 306 optimal weight: 0.2980 chunk 232 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN C 217 GLN H 76 ASN I 45 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN Q 44 GLN W 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 45083 Z= 0.332 Angle : 0.595 16.433 61281 Z= 0.302 Chirality : 0.044 0.217 6836 Planarity : 0.004 0.057 7603 Dihedral : 12.808 77.590 6790 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.76 % Allowed : 17.69 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.56 (0.12), residues: 5187 helix: 1.10 (0.12), residues: 1943 sheet: 0.48 (0.18), residues: 831 loop : -0.17 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 453 HIS 0.017 0.001 HIS M 18 PHE 0.028 0.002 PHE Q 146 TYR 0.019 0.002 TYR B 84 ARG 0.016 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 582 time to evaluate : 5.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7459 (mmtt) REVERT: A 266 MET cc_start: 0.4421 (OUTLIER) cc_final: 0.3724 (pmt) REVERT: A 410 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7681 (m-40) REVERT: A 613 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 660 MET cc_start: 0.8812 (mmm) cc_final: 0.8530 (mmt) REVERT: A 695 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: A 1015 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: A 1071 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: A 1224 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6572 (mtt180) REVERT: B 111 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 358 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6643 (pt0) REVERT: B 388 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8112 (t80) REVERT: B 578 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7940 (mmtt) REVERT: B 918 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8506 (p90) REVERT: C 89 THR cc_start: 0.8326 (p) cc_final: 0.8055 (p) REVERT: C 91 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6240 (mm-30) REVERT: C 210 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: K 22 ASN cc_start: 0.7995 (m-40) cc_final: 0.7709 (m-40) REVERT: L 58 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7121 (mmm-85) REVERT: M 44 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7395 (mtt180) REVERT: U 51 MET cc_start: 0.3252 (mmp) cc_final: 0.1695 (mpp) outliers start: 128 outliers final: 70 residues processed: 656 average time/residue: 1.6896 time to fit residues: 1353.1721 Evaluate side-chains 657 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 571 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 311 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 319 optimal weight: 0.5980 chunk 342 optimal weight: 0.0970 chunk 248 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 395 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 145 GLN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN H 76 ASN I 45 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45083 Z= 0.203 Angle : 0.556 10.328 61281 Z= 0.283 Chirality : 0.042 0.208 6836 Planarity : 0.004 0.057 7603 Dihedral : 12.791 77.738 6790 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.41 % Allowed : 18.23 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.66 (0.12), residues: 5187 helix: 1.23 (0.12), residues: 1934 sheet: 0.52 (0.18), residues: 828 loop : -0.15 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 453 HIS 0.014 0.001 HIS M 18 PHE 0.032 0.001 PHE Q 146 TYR 0.017 0.001 TYR B 215 ARG 0.012 0.000 ARG B1085 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 595 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7402 (mmtt) REVERT: A 266 MET cc_start: 0.4527 (ppp) cc_final: 0.3831 (pmt) REVERT: A 410 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7602 (m-40) REVERT: A 695 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: A 1015 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 1071 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 1224 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6584 (mtt180) REVERT: B 111 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8368 (t0) REVERT: B 358 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6665 (pt0) REVERT: B 388 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 578 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7878 (mmtt) REVERT: B 673 VAL cc_start: 0.8960 (t) cc_final: 0.8719 (m) REVERT: C 89 THR cc_start: 0.8372 (p) cc_final: 0.8136 (p) REVERT: C 210 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: G 1 MET cc_start: 0.4907 (pmm) cc_final: 0.4073 (ppp) REVERT: K 22 ASN cc_start: 0.8016 (m-40) cc_final: 0.7711 (m-40) REVERT: L 58 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6942 (mmm-85) REVERT: M 44 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7260 (mtt180) REVERT: M 277 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8268 (mm) REVERT: U 51 MET cc_start: 0.3200 (mmp) cc_final: 0.1581 (mpp) REVERT: W 76 MET cc_start: 0.1744 (mmm) cc_final: -0.2353 (mtm) outliers start: 112 outliers final: 61 residues processed: 660 average time/residue: 1.6717 time to fit residues: 1356.9940 Evaluate side-chains 650 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 576 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 457 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 chunk 468 optimal weight: 7.9990 chunk 481 optimal weight: 50.0000 chunk 282 optimal weight: 20.0000 chunk 204 optimal weight: 2.9990 chunk 368 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 423 optimal weight: 0.9980 chunk 443 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1129 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 430 ASN B1030 ASN B1049 GLN C 217 GLN H 76 ASN I 45 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN M 263 GLN M 271 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 45083 Z= 0.614 Angle : 0.716 18.054 61281 Z= 0.364 Chirality : 0.050 0.279 6836 Planarity : 0.006 0.090 7603 Dihedral : 12.993 77.664 6790 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.97 % Allowed : 17.91 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.26 (0.11), residues: 5187 helix: 0.80 (0.12), residues: 1936 sheet: 0.38 (0.18), residues: 833 loop : -0.33 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 453 HIS 0.018 0.002 HIS M 18 PHE 0.041 0.003 PHE Q 146 TYR 0.025 0.002 TYR B1048 ARG 0.017 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 580 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7540 (mmtt) REVERT: A 266 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3681 (pmt) REVERT: A 360 ASP cc_start: 0.8257 (m-30) cc_final: 0.7991 (m-30) REVERT: A 410 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: A 613 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: A 1015 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: A 1035 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: A 1071 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: A 1224 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6715 (mtt180) REVERT: A 1306 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7414 (ttmm) REVERT: A 1380 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7047 (mtp180) REVERT: B 28 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9030 (mt) REVERT: B 111 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 254 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5297 (mp10) REVERT: B 388 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8222 (t80) REVERT: B 918 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8702 (p90) REVERT: B 1109 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: C 89 THR cc_start: 0.8402 (p) cc_final: 0.8169 (p) REVERT: C 91 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6269 (mm-30) REVERT: C 210 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: G 1 MET cc_start: 0.4913 (pmm) cc_final: 0.4067 (ppp) REVERT: K 22 ASN cc_start: 0.8104 (m-40) cc_final: 0.7833 (m-40) REVERT: L 58 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7451 (mmm-85) REVERT: M 44 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7445 (mtt180) REVERT: O 293 TYR cc_start: 0.7313 (t80) cc_final: 0.7073 (t80) REVERT: Q 105 LYS cc_start: 0.4515 (mmtm) cc_final: 0.4298 (tppt) REVERT: U 51 MET cc_start: 0.3141 (mmp) cc_final: 0.1519 (mpp) outliers start: 138 outliers final: 83 residues processed: 664 average time/residue: 1.7456 time to fit residues: 1422.5225 Evaluate side-chains 675 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 572 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1109 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 467 optimal weight: 20.0000 chunk 307 optimal weight: 0.6980 chunk 495 optimal weight: 40.0000 chunk 302 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 520 optimal weight: 20.0000 chunk 478 optimal weight: 40.0000 chunk 414 optimal weight: 0.0470 chunk 42 optimal weight: 0.3980 chunk 319 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 430 ASN B1030 ASN C 217 GLN H 76 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 45083 Z= 0.225 Angle : 0.595 13.143 61281 Z= 0.302 Chirality : 0.043 0.297 6836 Planarity : 0.004 0.066 7603 Dihedral : 12.928 78.047 6790 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.96 % Allowed : 19.13 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.47 (0.12), residues: 5187 helix: 1.06 (0.12), residues: 1929 sheet: 0.37 (0.18), residues: 843 loop : -0.23 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 453 HIS 0.013 0.001 HIS M 18 PHE 0.034 0.001 PHE Q 146 TYR 0.020 0.001 TYR M 259 ARG 0.014 0.001 ARG A1153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 588 time to evaluate : 5.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7439 (mmtt) REVERT: A 266 MET cc_start: 0.4418 (ppp) cc_final: 0.3671 (pmt) REVERT: A 410 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7599 (m-40) REVERT: A 613 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: A 695 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: A 1015 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: A 1035 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: A 1071 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: A 1224 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6614 (mtt180) REVERT: B 111 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8377 (t0) REVERT: B 358 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: B 388 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8145 (t80) REVERT: B 673 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8713 (m) REVERT: B 1054 MET cc_start: 0.8699 (mpp) cc_final: 0.8361 (mtm) REVERT: B 1072 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8325 (tpt170) REVERT: C 89 THR cc_start: 0.8353 (p) cc_final: 0.8120 (p) REVERT: C 210 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: G 1 MET cc_start: 0.4811 (pmm) cc_final: 0.4065 (ppp) REVERT: K 22 ASN cc_start: 0.7991 (m-40) cc_final: 0.7701 (m-40) REVERT: L 58 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7178 (mmm-85) REVERT: M 277 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8267 (mm) REVERT: U 51 MET cc_start: 0.3187 (mmp) cc_final: 0.1501 (mpp) outliers start: 91 outliers final: 60 residues processed: 645 average time/residue: 1.7102 time to fit residues: 1345.4829 Evaluate side-chains 654 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 579 time to evaluate : 4.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1224 ARG Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 223 CYS Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 312 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 174 LYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain W residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 253 optimal weight: 0.6980 chunk 328 optimal weight: 0.6980 chunk 441 optimal weight: 30.0000 chunk 126 optimal weight: 0.6980 chunk 381 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 414 optimal weight: 0.0030 chunk 173 optimal weight: 4.9990 chunk 425 optimal weight: 0.0050 chunk 52 optimal weight: 0.9980 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 757 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN I 45 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN M 271 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.220506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166403 restraints weight = 49873.703| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45083 Z= 0.178 Angle : 0.575 15.914 61281 Z= 0.291 Chirality : 0.042 0.240 6836 Planarity : 0.004 0.060 7603 Dihedral : 12.846 77.047 6790 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.64 % Allowed : 19.63 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.63 (0.12), residues: 5187 helix: 1.23 (0.12), residues: 1924 sheet: 0.48 (0.18), residues: 816 loop : -0.17 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 453 HIS 0.011 0.001 HIS M 18 PHE 0.019 0.001 PHE B 918 TYR 0.019 0.001 TYR G 72 ARG 0.013 0.000 ARG A1153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19738.92 seconds wall clock time: 351 minutes 50.19 seconds (21110.19 seconds total)