Starting phenix.real_space_refine on Fri Jan 16 12:59:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p69_13222/01_2026/7p69_13222.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.020 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 Ca 1 9.91 5 Fe 32 7.16 5 P 15 5.49 5 S 264 5.16 5 C 24122 2.51 5 N 6072 2.21 5 O 7071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37577 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4597 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 157} Chain breaks: 2 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2422 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4595 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 582} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "L" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 341 Unusual residues: {'3PE': 6, 'LFA': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 76.148 59.075 197.648 1.00 23.25 S ATOM 2766 SG CYS F 357 79.740 58.726 201.931 1.00 41.84 S ATOM 3087 SG CYS F 398 74.089 55.086 202.563 1.00 29.31 S ATOM 2722 SG CYS F 351 78.534 52.827 198.822 1.00 17.57 S ATOM 4079 SG CYS E 92 88.002 51.072 218.313 1.00 47.18 S ATOM 4113 SG CYS E 97 88.153 51.870 221.755 1.00 41.18 S ATOM 4391 SG CYS E 133 82.823 50.276 218.007 1.00 38.35 S ATOM 4417 SG CYS E 137 82.007 50.965 221.245 1.00 47.14 S ATOM 5501 SG CYS G 114 85.724 65.599 179.734 1.00 15.40 S ATOM 5441 SG CYS G 105 90.786 69.728 181.028 1.00 11.56 S ATOM 5461 SG CYS G 108 91.726 63.722 178.840 1.00 8.68 S ATOM 5855 SG CYS G 156 80.494 57.545 184.886 1.00 11.24 S ATOM 5836 SG CYS G 153 86.476 56.663 187.713 1.00 7.17 S ATOM 5884 SG CYS G 159 83.726 51.987 184.288 1.00 9.55 S ATOM 6228 SG CYS G 203 85.506 57.279 181.093 1.00 3.10 S ATOM 6453 SG CYS G 230 81.954 48.615 160.093 1.00 12.71 S ATOM 6738 SG CYS G 265 82.246 44.835 165.451 1.00 10.51 S ATOM 6501 SG CYS G 237 76.734 48.102 163.418 1.00 14.02 S ATOM 6477 SG CYS G 233 79.056 42.812 160.323 1.00 10.80 S ATOM 4902 SG CYS G 36 74.004 58.213 187.938 1.00 10.53 S ATOM 4978 SG CYS G 47 75.513 61.687 188.172 1.00 8.48 S ATOM 5004 SG CYS G 50 69.713 63.073 188.318 1.00 18.54 S ATOM 5153 SG CYS G 69 69.301 59.468 187.951 1.00 19.72 S ATOM 16888 SG CYS B 129 94.274 93.266 155.492 1.00 40.63 S ATOM 16524 SG CYS B 64 99.323 97.288 156.876 1.00 86.94 S ATOM 16518 SG CYS B 63 93.495 99.049 158.693 1.00 79.18 S ATOM 17105 SG CYS B 158 96.307 93.439 161.181 1.00 54.13 S ATOM 18149 SG CYS I 102 95.274 87.493 167.163 1.00 8.14 S ATOM 18124 SG CYS I 99 100.707 86.324 163.453 1.00 12.95 S ATOM 18167 SG CYS I 105 99.508 83.029 168.946 1.00 11.38 S ATOM 17882 SG CYS I 70 95.553 82.149 163.901 1.00 8.76 S ATOM 18196 SG CYS I 109 100.937 77.618 175.221 1.00 12.77 S ATOM 17859 SG CYS I 66 98.847 76.760 169.170 1.00 11.64 S ATOM 17819 SG CYS I 60 103.226 72.698 171.329 1.00 14.82 S ATOM 17837 SG CYS I 63 97.030 72.922 174.041 1.00 11.28 S Time building chain proxies: 8.06, per 1000 atoms: 0.21 Number of scatterers: 37577 At special positions: 0 Unit cell: (158.5, 210.5, 251.5, 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) Fe 32 26.01 Ca 1 19.99 S 264 16.00 P 15 15.00 O 7071 8.00 N 6072 7.00 C 24122 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 - 3.00 Amino acid : True - 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: 3.65 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 53.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.666A pdb=" N ASP F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.592A pdb=" N SER E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.137A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.812A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 276 removed outlier: 5.062A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.278A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.571A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 605 removed outlier: 5.015A pdb=" N ASN G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.354A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP G 690 " --> pdb=" O ALA G 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 683 through 690' Processing helix chain 'G' and resid 764 through 768 removed outlier: 5.101A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 768' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.108A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.922A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 56 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.938A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.612A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.085A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 231 through 257 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 removed outlier: 4.881A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'L' and resid 4 through 20 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.469A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 4.895A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 233 Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 256 through 262 Processing helix chain 'M' and resid 266 through 275 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 501 removed outlier: 4.859A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.457A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 5.149A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.369A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.047A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1685 hydrogen bonds defined for protein. 5055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15652 1.42 - 1.64: 21757 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37904 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.383 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.371 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.608 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.382 0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" O13 3PE L 705 " pdb=" P 3PE L 705 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.13e+00 ... (remaining 37899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 50648 2.54 - 5.09: 597 5.09 - 7.63: 93 7.63 - 10.17: 15 10.17 - 12.71: 3 Bond angle restraints: 51356 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.10 12.71 2.21e+00 2.05e-01 3.31e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.82 -12.02 2.44e+00 1.68e-01 2.43e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" CB THR N 64 " ideal model delta sigma weight residual 110.37 118.44 -8.07 1.78e+00 3.16e-01 2.06e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 angle pdb=" S3 SF4 F 501 " pdb="FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.12 -6.02 1.50e+00 4.44e-01 1.61e+01 ... (remaining 51351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 21466 23.95 - 47.90: 796 47.90 - 71.85: 145 71.85 - 95.80: 20 95.80 - 119.75: 6 Dihedral angle restraints: 22433 sinusoidal: 9169 harmonic: 13264 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.56 44.44 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual -180.00 -145.16 -34.84 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.80 34.20 0 5.00e+00 4.00e-02 4.68e+01 ... (remaining 22430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5686 4.238 - 8.477: 0 8.477 - 12.715: 0 12.715 - 16.953: 0 16.953 - 21.191: 28 Chirality restraints: 5714 Sorted by residual: chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5711 not shown) Planarity restraints: 6392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO N 5 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C VAL N 63 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.021 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 260 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C ASN G 260 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN G 260 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS G 261 " -0.015 2.00e-02 2.50e+03 ... (remaining 6389 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2271 2.73 - 3.27: 37563 3.27 - 3.82: 69072 3.82 - 4.36: 87232 4.36 - 4.90: 143241 Nonbonded interactions: 339379 Sorted by model distance: nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.221 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.265 3.040 ... (remaining 339374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.030 Extract box with map and model: 2.890 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 : 0.007 0.205 37940 Z= 0.275 Angle : 0.756 13.714 51449 Z= 0.381 Chirality : 1.479 21.191 5714 Planarity : 0.006 0.085 6392 Dihedral : 13.231 119.753 13949 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 2.11 % Allowed : 4.91 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4601 helix: 0.35 (0.09), residues: 2663 sheet: -0.36 (0.29), residues: 318 loop : -0.69 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 152 TYR 0.031 0.002 TYR L 428 PHE 0.040 0.002 PHE L 341 TRP 0.024 0.002 TRP L 143 HIS 0.006 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.00625 (37904) covalent geometry : angle 0.73569 (51356) hydrogen bonds : bond 0.06791 ( 1685) hydrogen bonds : angle 4.78781 ( 5055) metal coordination : bond 0.05887 ( 36) metal coordination : angle 4.12724 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 609 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: F 387 LEU cc_start: 0.8667 (mt) cc_final: 0.8453 (mp) REVERT: E 114 ASN cc_start: 0.8776 (m-40) cc_final: 0.8535 (m110) REVERT: G 64 ARG cc_start: 0.8865 (ttp-110) cc_final: 0.8530 (ptt-90) REVERT: G 88 GLN cc_start: 0.9099 (mt0) cc_final: 0.8722 (mm-40) REVERT: G 375 ASP cc_start: 0.8777 (m-30) cc_final: 0.8331 (t0) REVERT: G 586 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8711 (mp) REVERT: G 854 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8016 (m) REVERT: G 874 GLU cc_start: 0.9062 (tt0) cc_final: 0.8581 (tp30) REVERT: C 191 ASP cc_start: 0.7508 (m-30) cc_final: 0.7208 (m-30) REVERT: C 482 GLU cc_start: 0.9012 (tp30) cc_final: 0.8491 (tm-30) REVERT: B 52 ASN cc_start: 0.9123 (m110) cc_final: 0.8866 (m110) REVERT: B 68 MET cc_start: 0.5672 (tpt) cc_final: 0.5420 (mmm) REVERT: I 83 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8561 (mppt) REVERT: I 162 ASP cc_start: 0.8117 (t70) cc_final: 0.7915 (t70) REVERT: I 174 ASP cc_start: 0.9053 (t70) cc_final: 0.8840 (t0) REVERT: H 228 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 94 GLU cc_start: 0.9285 (mp0) cc_final: 0.9042 (mp0) REVERT: L 51 ASP cc_start: 0.8910 (t0) cc_final: 0.8707 (t0) REVERT: L 360 GLN cc_start: 0.5300 (mt0) cc_final: 0.4579 (mt0) REVERT: M 165 LYS cc_start: 0.8397 (tttm) cc_final: 0.8190 (ttpp) REVERT: M 263 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7891 (tp) REVERT: M 451 GLN cc_start: 0.8690 (mm110) cc_final: 0.8479 (tp40) REVERT: N 485 MET cc_start: 0.3922 (mmp) cc_final: 0.3143 (mmt) REVERT: K 26 ARG cc_start: 0.9033 (ttp-170) cc_final: 0.8805 (ttp-110) REVERT: J 94 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8108 (mt) outliers start: 80 outliers final: 19 residues processed: 666 average time/residue: 0.7680 time to fit residues: 615.6845 Evaluate side-chains 517 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 494 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 43 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 341 ASN F 386 GLN E 98 HIS G 54 GLN G 57 ASN G 218 ASN G 238 ASN G 490 GLN G 583 ASN G 745 GLN G 901 HIS C 317 ASN C 344 GLN H 113 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN A 13 HIS L 326 GLN L 524 ASN N 149 GLN N 199 ASN N 404 GLN K 82 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062833 restraints weight = 46951.574| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.15 r_work: 0.2612 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37940 Z= 0.417 Angle : 2.509 50.974 51449 Z= 1.444 Chirality : 0.451 6.672 5714 Planarity : 0.005 0.074 6392 Dihedral : 9.660 119.551 5792 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 2.48 % Allowed : 9.67 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4601 helix: 1.03 (0.10), residues: 2682 sheet: -0.34 (0.30), residues: 317 loop : -0.49 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.023 0.002 TYR L 428 PHE 0.028 0.002 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01179 (37904) covalent geometry : angle 2.19213 (51356) hydrogen bonds : bond 0.05862 ( 1685) hydrogen bonds : angle 4.35357 ( 5055) metal coordination : bond 0.05478 ( 36) metal coordination : angle 28.80820 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 514 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8698 (m-40) cc_final: 0.8481 (m110) REVERT: E 125 ARG cc_start: 0.9108 (ttt180) cc_final: 0.8859 (ttt180) REVERT: G 129 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (ptt180) REVERT: G 426 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8135 (mtp85) REVERT: G 586 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8787 (mp) REVERT: G 626 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: G 750 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7929 (ppt-90) REVERT: G 806 GLN cc_start: 0.8715 (mm110) cc_final: 0.8417 (mm110) REVERT: C 356 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7984 (t80) REVERT: C 475 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8501 (ttm110) REVERT: I 162 ASP cc_start: 0.8135 (t70) cc_final: 0.7849 (t70) REVERT: H 228 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7658 (mm-30) REVERT: L 32 ILE cc_start: 0.8931 (pt) cc_final: 0.8671 (mt) REVERT: L 360 GLN cc_start: 0.5721 (mt0) cc_final: 0.5041 (mt0) REVERT: L 424 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7668 (mmt) REVERT: M 263 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7855 (tp) REVERT: N 200 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: N 462 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (mp) REVERT: N 485 MET cc_start: 0.4507 (mmp) cc_final: 0.3592 (mmt) REVERT: K 87 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7306 (mpt180) outliers start: 94 outliers final: 28 residues processed: 575 average time/residue: 0.7672 time to fit residues: 529.0968 Evaluate side-chains 520 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 481 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 273 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS G 88 GLN G 583 ASN G 901 HIS C 344 GLN B 52 ASN B 213 ASN H 113 ASN H 152 GLN H 183 GLN H 188 ASN L 524 ASN N 149 GLN N 199 ASN K 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.062803 restraints weight = 47124.417| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.14 r_work: 0.2610 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37940 Z= 0.410 Angle : 2.503 50.604 51449 Z= 1.442 Chirality : 0.450 6.592 5714 Planarity : 0.005 0.070 6392 Dihedral : 9.432 117.999 5769 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 2.69 % Allowed : 10.78 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4601 helix: 1.32 (0.10), residues: 2669 sheet: -0.25 (0.30), residues: 315 loop : -0.31 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 64 TYR 0.022 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01171 (37904) covalent geometry : angle 2.18754 (51356) hydrogen bonds : bond 0.05678 ( 1685) hydrogen bonds : angle 4.26523 ( 5055) metal coordination : bond 0.04863 ( 36) metal coordination : angle 28.71084 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 496 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: F 387 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (mp) REVERT: E 114 ASN cc_start: 0.8711 (m-40) cc_final: 0.8482 (m110) REVERT: E 125 ARG cc_start: 0.9147 (ttt180) cc_final: 0.8943 (ttt-90) REVERT: G 129 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8696 (ptt90) REVERT: G 426 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: G 586 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8773 (mp) REVERT: G 806 GLN cc_start: 0.8715 (mm110) cc_final: 0.8444 (mm110) REVERT: G 854 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8662 (m) REVERT: C 191 ASP cc_start: 0.7589 (m-30) cc_final: 0.7267 (m-30) REVERT: C 475 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8474 (ttm110) REVERT: I 126 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8769 (mptm) REVERT: H 228 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7671 (mm-30) REVERT: L 178 ASP cc_start: 0.8358 (m-30) cc_final: 0.7949 (m-30) REVERT: L 360 GLN cc_start: 0.5700 (mt0) cc_final: 0.5027 (mt0) REVERT: M 110 GLU cc_start: 0.8190 (mp0) cc_final: 0.7912 (mp0) REVERT: M 263 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7829 (tp) REVERT: N 200 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: N 462 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8897 (mp) REVERT: N 485 MET cc_start: 0.4424 (mmp) cc_final: 0.3542 (mmt) REVERT: K 87 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7378 (mpt180) outliers start: 102 outliers final: 42 residues processed: 563 average time/residue: 0.7537 time to fit residues: 511.4791 Evaluate side-chains 525 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 473 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 26 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 400 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 425 GLN E 98 HIS G 224 GLN G 345 HIS G 583 ASN G 768 ASN G 901 HIS C 236 GLN C 344 GLN B 52 ASN B 213 ASN H 113 ASN H 226 HIS L 58 GLN L 358 HIS L 524 ASN M 198 ASN N 199 ASN K 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.059928 restraints weight = 46691.968| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 1.14 r_work: 0.2542 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.239 37940 Z= 0.513 Angle : 2.532 50.541 51449 Z= 1.455 Chirality : 0.458 6.785 5714 Planarity : 0.006 0.076 6392 Dihedral : 10.461 122.656 5764 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 3.09 % Allowed : 11.02 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4601 helix: 1.09 (0.10), residues: 2676 sheet: -0.28 (0.29), residues: 321 loop : -0.29 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 59 TYR 0.022 0.002 TYR H 242 PHE 0.030 0.002 PHE I 101 TRP 0.025 0.002 TRP L 143 HIS 0.009 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01370 (37904) covalent geometry : angle 2.22269 (51356) hydrogen bonds : bond 0.07463 ( 1685) hydrogen bonds : angle 4.60983 ( 5055) metal coordination : bond 0.06282 ( 36) metal coordination : angle 28.61685 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 479 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8791 (m-40) cc_final: 0.8564 (m110) REVERT: G 129 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8468 (ptm-80) REVERT: G 158 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7990 (mtp180) REVERT: G 426 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8138 (mtp85) REVERT: G 586 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8755 (mp) REVERT: G 750 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8068 (ppt-90) REVERT: G 834 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: G 854 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 191 ASP cc_start: 0.7606 (m-30) cc_final: 0.7273 (m-30) REVERT: C 475 ARG cc_start: 0.8724 (ttm110) cc_final: 0.8454 (ttm110) REVERT: C 482 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: I 126 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8853 (mptm) REVERT: H 197 ILE cc_start: 0.9128 (pt) cc_final: 0.8885 (mt) REVERT: H 228 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7722 (mm-30) REVERT: H 261 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8407 (mt0) REVERT: L 178 ASP cc_start: 0.8337 (m-30) cc_final: 0.8009 (m-30) REVERT: L 360 GLN cc_start: 0.5877 (mt0) cc_final: 0.5156 (mt0) REVERT: M 110 GLU cc_start: 0.8206 (mp0) cc_final: 0.7955 (mp0) REVERT: M 263 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7918 (tp) REVERT: N 61 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.7824 (pmm) REVERT: N 200 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: K 5 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8775 (mp10) outliers start: 117 outliers final: 49 residues processed: 552 average time/residue: 0.8017 time to fit residues: 529.2021 Evaluate side-chains 525 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 462 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 261 GLN Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 371 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 98 HIS G 583 ASN C 344 GLN B 52 ASN B 213 ASN H 113 ASN L 28 ASN L 58 GLN L 358 HIS L 524 ASN M 455 GLN N 199 ASN K 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.063281 restraints weight = 46659.876| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.14 r_work: 0.2624 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37940 Z= 0.396 Angle : 2.503 50.599 51449 Z= 1.442 Chirality : 0.447 6.513 5714 Planarity : 0.004 0.071 6392 Dihedral : 9.760 121.948 5764 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 2.75 % Allowed : 11.81 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 4601 helix: 1.41 (0.10), residues: 2673 sheet: -0.23 (0.30), residues: 316 loop : -0.19 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 64 TYR 0.023 0.001 TYR L 428 PHE 0.043 0.001 PHE K 46 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01148 (37904) covalent geometry : angle 2.18488 (51356) hydrogen bonds : bond 0.05354 ( 1685) hydrogen bonds : angle 4.25265 ( 5055) metal coordination : bond 0.03614 ( 36) metal coordination : angle 28.81067 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 492 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8761 (m-40) cc_final: 0.8534 (m110) REVERT: G 158 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7867 (mtp180) REVERT: G 426 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8058 (mtp85) REVERT: G 586 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8729 (mp) REVERT: G 750 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7979 (ppt-90) REVERT: G 854 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8661 (m) REVERT: C 191 ASP cc_start: 0.7595 (m-30) cc_final: 0.7289 (m-30) REVERT: H 228 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7706 (mm-30) REVERT: L 178 ASP cc_start: 0.8186 (m-30) cc_final: 0.7932 (m-30) REVERT: L 360 GLN cc_start: 0.5596 (mt0) cc_final: 0.4906 (mt0) REVERT: M 110 GLU cc_start: 0.8200 (mp0) cc_final: 0.7947 (mp0) REVERT: M 263 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7788 (tp) REVERT: M 407 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: N 200 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: K 46 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8237 (t80) REVERT: J 103 MET cc_start: 0.9100 (ttp) cc_final: 0.8884 (ttt) REVERT: J 116 ASP cc_start: 0.8902 (t0) cc_final: 0.8639 (t0) outliers start: 104 outliers final: 44 residues processed: 560 average time/residue: 0.7833 time to fit residues: 526.6487 Evaluate side-chains 526 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 473 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 432 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 126 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 323 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 423 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 583 ASN C 344 GLN B 52 ASN B 213 ASN H 113 ASN H 261 GLN L 58 GLN L 358 HIS L 524 ASN N 199 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.064297 restraints weight = 47012.135| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.14 r_work: 0.2645 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37940 Z= 0.390 Angle : 2.499 50.607 51449 Z= 1.440 Chirality : 0.446 6.497 5714 Planarity : 0.004 0.069 6392 Dihedral : 9.284 120.362 5763 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 12.50 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 4601 helix: 1.62 (0.10), residues: 2663 sheet: -0.23 (0.30), residues: 320 loop : -0.12 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 664 TYR 0.023 0.001 TYR H 242 PHE 0.027 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01137 (37904) covalent geometry : angle 2.18007 (51356) hydrogen bonds : bond 0.04947 ( 1685) hydrogen bonds : angle 4.10628 ( 5055) metal coordination : bond 0.03442 ( 36) metal coordination : angle 28.81507 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 500 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8759 (m-40) cc_final: 0.8532 (m110) REVERT: G 158 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: G 426 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8054 (mtp85) REVERT: G 626 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: G 750 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7935 (ppt-90) REVERT: G 854 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 191 ASP cc_start: 0.7541 (m-30) cc_final: 0.7257 (m-30) REVERT: C 475 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8306 (ttm-80) REVERT: C 482 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: H 58 LEU cc_start: 0.8156 (mm) cc_final: 0.7936 (mt) REVERT: H 228 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7653 (mm-30) REVERT: L 144 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8394 (mm-30) REVERT: L 178 ASP cc_start: 0.8149 (m-30) cc_final: 0.7879 (m-30) REVERT: L 360 GLN cc_start: 0.5501 (mt0) cc_final: 0.4845 (mt0) REVERT: L 493 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8623 (tm) REVERT: M 110 GLU cc_start: 0.8228 (mp0) cc_final: 0.7967 (mp0) REVERT: N 200 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: K 87 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7307 (mpt180) REVERT: J 103 MET cc_start: 0.9091 (ttp) cc_final: 0.8870 (ttt) outliers start: 99 outliers final: 40 residues processed: 562 average time/residue: 0.7714 time to fit residues: 522.4232 Evaluate side-chains 528 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 77 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 457 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 403 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN G 583 ASN C 283 ASN C 344 GLN B 213 ASN H 113 ASN L 58 GLN L 358 HIS L 524 ASN N 199 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.061781 restraints weight = 46644.808| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.14 r_work: 0.2586 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37940 Z= 0.426 Angle : 2.511 50.555 51449 Z= 1.445 Chirality : 0.451 6.626 5714 Planarity : 0.005 0.067 6392 Dihedral : 9.546 122.857 5757 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.59 % Allowed : 12.87 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4601 helix: 1.45 (0.10), residues: 2681 sheet: -0.19 (0.30), residues: 311 loop : -0.12 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 64 TYR 0.029 0.002 TYR H 242 PHE 0.026 0.002 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01199 (37904) covalent geometry : angle 2.19633 (51356) hydrogen bonds : bond 0.06054 ( 1685) hydrogen bonds : angle 4.30267 ( 5055) metal coordination : bond 0.04915 ( 36) metal coordination : angle 28.70793 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 475 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8788 (m-40) cc_final: 0.8550 (m110) REVERT: G 426 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8105 (mtp85) REVERT: G 750 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8013 (ppt-90) REVERT: G 854 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8738 (m) REVERT: C 191 ASP cc_start: 0.7564 (m-30) cc_final: 0.7272 (m-30) REVERT: C 482 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: H 228 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7634 (mm-30) REVERT: L 178 ASP cc_start: 0.8189 (m-30) cc_final: 0.7908 (m-30) REVERT: L 360 GLN cc_start: 0.5593 (mt0) cc_final: 0.4918 (mt0) REVERT: M 48 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8674 (mp) REVERT: M 110 GLU cc_start: 0.8268 (mp0) cc_final: 0.8056 (mp0) REVERT: M 407 GLU cc_start: 0.7929 (tp30) cc_final: 0.7659 (mt-10) REVERT: N 200 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: K 87 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7427 (mpt180) outliers start: 98 outliers final: 46 residues processed: 540 average time/residue: 0.7862 time to fit residues: 508.3526 Evaluate side-chains 520 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 467 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 4 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 423 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN G 583 ASN G 765 GLN C 344 GLN B 213 ASN H 113 ASN L 58 GLN L 358 HIS L 524 ASN N 199 ASN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.064148 restraints weight = 46785.562| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.14 r_work: 0.2642 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 37940 Z= 0.390 Angle : 2.502 50.575 51449 Z= 1.441 Chirality : 0.446 6.483 5714 Planarity : 0.004 0.069 6392 Dihedral : 9.186 121.505 5757 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 2.09 % Allowed : 13.58 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.12), residues: 4601 helix: 1.65 (0.10), residues: 2661 sheet: -0.12 (0.30), residues: 313 loop : -0.09 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 64 TYR 0.022 0.001 TYR L 428 PHE 0.027 0.001 PHE L 341 TRP 0.020 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01137 (37904) covalent geometry : angle 2.18313 (51356) hydrogen bonds : bond 0.05017 ( 1685) hydrogen bonds : angle 4.13341 ( 5055) metal coordination : bond 0.03378 ( 36) metal coordination : angle 28.84902 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8778 (m-40) cc_final: 0.8548 (m110) REVERT: G 426 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8057 (mtp85) REVERT: G 750 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7992 (ppt-90) REVERT: G 854 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8706 (m) REVERT: C 191 ASP cc_start: 0.7539 (m-30) cc_final: 0.7267 (m-30) REVERT: C 482 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: H 228 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7625 (mm-30) REVERT: L 48 ILE cc_start: 0.9106 (mt) cc_final: 0.8812 (mp) REVERT: L 144 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8404 (mm-30) REVERT: L 178 ASP cc_start: 0.8137 (m-30) cc_final: 0.7829 (m-30) REVERT: L 360 GLN cc_start: 0.5485 (mt0) cc_final: 0.4831 (mt0) REVERT: L 493 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (tm) REVERT: M 110 GLU cc_start: 0.8261 (mp0) cc_final: 0.8054 (mp0) REVERT: M 407 GLU cc_start: 0.7843 (tp30) cc_final: 0.7586 (mt-10) REVERT: N 200 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: K 87 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7300 (mpt180) REVERT: J 103 MET cc_start: 0.9113 (ttp) cc_final: 0.8892 (ttt) outliers start: 79 outliers final: 50 residues processed: 539 average time/residue: 0.7780 time to fit residues: 504.4524 Evaluate side-chains 535 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 478 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 165 optimal weight: 10.0000 chunk 355 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 278 optimal weight: 9.9990 chunk 395 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 381 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN G 218 ASN G 583 ASN C 154 ASN C 344 GLN B 213 ASN L 358 HIS L 524 ASN N 199 ASN K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.063922 restraints weight = 47196.751| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.14 r_work: 0.2636 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 37940 Z= 0.393 Angle : 2.504 50.565 51449 Z= 1.442 Chirality : 0.447 6.505 5714 Planarity : 0.004 0.067 6392 Dihedral : 9.079 121.365 5757 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 13.58 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 4601 helix: 1.66 (0.10), residues: 2664 sheet: -0.09 (0.30), residues: 313 loop : -0.08 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 64 TYR 0.028 0.001 TYR H 242 PHE 0.026 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01143 (37904) covalent geometry : angle 2.18660 (51356) hydrogen bonds : bond 0.05087 ( 1685) hydrogen bonds : angle 4.12401 ( 5055) metal coordination : bond 0.03681 ( 36) metal coordination : angle 28.79935 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 490 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8783 (m-40) cc_final: 0.8551 (m110) REVERT: G 426 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: G 626 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: G 750 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7923 (ppt-90) REVERT: G 854 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8727 (m) REVERT: C 191 ASP cc_start: 0.7543 (m-30) cc_final: 0.7268 (m-30) REVERT: C 482 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: I 126 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8775 (mptm) REVERT: H 228 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7641 (mm-30) REVERT: L 48 ILE cc_start: 0.9093 (mt) cc_final: 0.8798 (mp) REVERT: L 178 ASP cc_start: 0.8136 (m-30) cc_final: 0.7904 (m-30) REVERT: L 360 GLN cc_start: 0.5479 (mt0) cc_final: 0.4829 (mt0) REVERT: M 110 GLU cc_start: 0.8279 (mp0) cc_final: 0.8074 (mp0) REVERT: M 407 GLU cc_start: 0.7839 (tp30) cc_final: 0.7575 (mt-10) REVERT: N 200 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: K 87 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7322 (mpt180) REVERT: J 103 MET cc_start: 0.9113 (ttp) cc_final: 0.8878 (ttt) outliers start: 78 outliers final: 50 residues processed: 542 average time/residue: 0.7876 time to fit residues: 512.8357 Evaluate side-chains 536 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 478 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 225 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN E 98 HIS G 352 GLN G 583 ASN C 154 ASN C 344 GLN B 213 ASN L 58 GLN L 358 HIS L 524 ASN N 199 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.061650 restraints weight = 46798.856| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.14 r_work: 0.2584 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37940 Z= 0.438 Angle : 2.516 50.554 51449 Z= 1.447 Chirality : 0.454 6.653 5714 Planarity : 0.005 0.067 6392 Dihedral : 9.528 123.842 5757 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.82 % Allowed : 13.87 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4601 helix: 1.46 (0.10), residues: 2682 sheet: -0.13 (0.30), residues: 311 loop : -0.13 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 64 TYR 0.027 0.002 TYR H 242 PHE 0.026 0.002 PHE L 341 TRP 0.018 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01223 (37904) covalent geometry : angle 2.20277 (51356) hydrogen bonds : bond 0.06185 ( 1685) hydrogen bonds : angle 4.33634 ( 5055) metal coordination : bond 0.05340 ( 36) metal coordination : angle 28.66287 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 463 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8824 (m-40) cc_final: 0.8588 (m110) REVERT: G 426 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8112 (mtp85) REVERT: G 750 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8007 (ppt-90) REVERT: G 854 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8755 (m) REVERT: C 191 ASP cc_start: 0.7549 (m-30) cc_final: 0.7280 (m-30) REVERT: C 482 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: I 126 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8806 (mptm) REVERT: H 228 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7671 (mm-30) REVERT: L 360 GLN cc_start: 0.5557 (mt0) cc_final: 0.4902 (mt0) REVERT: M 110 GLU cc_start: 0.8294 (mp0) cc_final: 0.8068 (mp0) REVERT: M 407 GLU cc_start: 0.7898 (tp30) cc_final: 0.7642 (mt-10) REVERT: N 200 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: J 103 MET cc_start: 0.9120 (ttp) cc_final: 0.8878 (ttt) outliers start: 69 outliers final: 49 residues processed: 511 average time/residue: 0.8142 time to fit residues: 498.1316 Evaluate side-chains 520 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 465 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 426 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 426 optimal weight: 0.8980 chunk 438 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 373 optimal weight: 0.9980 chunk 291 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN E 98 HIS G 583 ASN C 154 ASN C 344 GLN L 58 GLN L 121 ASN L 358 HIS L 524 ASN N 199 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.065544 restraints weight = 47118.075| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.14 r_work: 0.2675 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37940 Z= 0.387 Angle : 2.505 50.587 51449 Z= 1.442 Chirality : 0.445 6.432 5714 Planarity : 0.004 0.069 6392 Dihedral : 8.980 121.465 5757 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 14.24 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 4601 helix: 1.71 (0.10), residues: 2658 sheet: -0.07 (0.30), residues: 315 loop : -0.08 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 64 TYR 0.025 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01136 (37904) covalent geometry : angle 2.18474 (51356) hydrogen bonds : bond 0.04604 ( 1685) hydrogen bonds : angle 4.07398 ( 5055) metal coordination : bond 0.02898 ( 36) metal coordination : angle 28.91972 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27119.55 seconds wall clock time: 458 minutes 26.53 seconds (27506.53 seconds total)