Starting phenix.real_space_refine on Fri Jun 5 13:02:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tal_55750/06_2026/9tal_55750.map" } resolution = 2.66 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= -0.000 sd= 0.042 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 5 9.91 5 Fe 32 7.16 5 P 1 5.49 5 S 159 5.16 5 C 12737 2.51 5 N 3522 2.21 5 O 3969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20425 Number of models: 1 Model: "" Number of chains: 22 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: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} 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: "B" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1566 Classifications: {'peptide': 197} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 183} Chain breaks: 3 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 133 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "H" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "J" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "K" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 166 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 120 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' CA': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 31 Unusual residues: {' CA': 3, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' CA': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "G" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 647 SG CYS E 92 75.119 47.961 127.020 1.00 48.52 S ATOM 681 SG CYS E 97 76.542 45.630 129.285 1.00 57.56 S ATOM 959 SG CYS E 133 78.939 51.608 126.729 1.00 72.84 S ATOM 985 SG CYS E 137 81.088 49.475 127.974 1.00 59.04 S ATOM 3917 SG CYS F 351 73.704 60.862 109.961 1.00 37.71 S ATOM 3941 SG CYS F 354 76.844 58.187 104.658 1.00 42.62 S ATOM 3961 SG CYS F 357 76.343 54.870 108.478 1.00 47.21 S ATOM 4282 SG CYS F 398 79.805 60.177 110.229 1.00 37.53 S ATOM 6717 SG CYS G 265 51.527 80.505 90.984 1.00 37.65 S ATOM 6432 SG CYS G 230 50.466 80.561 84.711 1.00 49.26 S ATOM 6480 SG CYS G 237 56.211 82.336 86.487 1.00 42.09 S ATOM 6456 SG CYS G 233 51.165 85.984 87.992 1.00 49.10 S ATOM 5811 SG CYS G 153 62.688 59.400 100.649 1.00 49.49 S ATOM 6207 SG CYS G 203 60.475 62.718 95.220 1.00 35.27 S ATOM 5830 SG CYS G 156 66.346 63.231 96.881 1.00 38.54 S ATOM 5859 SG CYS G 159 61.875 65.624 100.745 1.00 35.75 S ATOM 4877 SG CYS G 36 73.555 64.939 97.343 1.00 39.30 S ATOM 4953 SG CYS G 47 73.573 61.642 95.688 1.00 29.41 S ATOM 4979 SG CYS G 50 78.255 63.913 93.412 1.00 41.93 S ATOM 5128 SG CYS G 69 77.843 66.824 95.751 1.00 54.90 S ATOM 5436 SG CYS G 108 56.442 56.006 90.690 1.00 50.82 S ATOM 5416 SG CYS G 105 60.078 51.121 88.070 1.00 36.39 S ATOM 5476 SG CYS G 114 62.176 57.327 89.014 1.00 38.90 S ATOM 11926 SG CYS I 70 51.645 47.789 68.242 1.00 43.28 S ATOM 11950 SG CYS I 74 49.721 47.153 67.367 1.00 66.40 S ATOM 12193 SG CYS I 102 54.947 42.954 67.104 1.00 44.05 S ATOM 12168 SG CYS I 99 48.538 42.324 66.101 1.00 38.91 S ATOM 12211 SG CYS I 105 51.062 42.542 71.979 1.00 48.13 S ATOM 11903 SG CYS I 66 49.724 47.491 76.415 1.00 43.36 S ATOM 11881 SG CYS I 63 52.377 48.547 82.042 1.00 33.11 S ATOM 12240 SG CYS I 109 51.464 42.829 80.575 1.00 44.02 S ATOM 11863 SG CYS I 60 46.048 46.734 81.382 1.00 35.64 S ATOM 13864 SG CYS B 158 52.972 41.250 58.872 1.00 44.57 S ATOM 13647 SG CYS B 129 52.344 44.948 54.736 1.00 43.03 S ATOM 13196 SG CYS B 64 50.042 38.827 53.755 1.00 57.89 S ATOM 13190 SG CYS B 63 56.390 39.849 53.467 1.00 61.19 S Time building chain proxies: 4.59, per 1000 atoms: 0.22 Number of scatterers: 20425 At special positions: 0 Unit cell: (120.45, 126.225, 157.575, 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 5 19.99 S 159 16.00 P 1 15.00 O 3969 8.00 N 3522 7.00 C 12737 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: 1.87 Conformation dependent library (CDL) restraints added in 915.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1003 " pdb="FE2 FES G1003 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1003 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1003 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1003 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 351 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 398 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 357 " pdb=" SF4 G1001 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1001 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 230 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1007 " pdb="FE1 SF4 G1007 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G1007 " - pdb=" SG CYS G 108 " pdb="FE3 SF4 G1007 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G1007 " - pdb=" SG CYS G 114 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 74 " pdb=" SF4 I 203 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 109 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " Number of angles added : 96 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 23 sheets defined 44.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 54 through 63 removed outlier: 4.869A pdb=" N ASP E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.554A pdb=" N VAL E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 113 removed outlier: 4.046A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 68 through 75 removed outlier: 3.718A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.982A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.787A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 removed outlier: 3.714A pdb=" N ILE F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.882A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.601A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 removed outlier: 3.636A pdb=" N TYR F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 removed outlier: 3.601A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 removed outlier: 3.559A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'F' and resid 405 through 415 Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.613A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 114 through 124 Processing helix chain 'G' and resid 150 through 153 Processing helix chain 'G' and resid 157 through 164 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.898A pdb=" N VAL G 181 " --> pdb=" O HIS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 211 through 216 removed outlier: 3.624A pdb=" N GLU G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 216' Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 265 through 271 Processing helix chain 'G' and resid 272 through 277 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'G' and resid 383 through 388 Processing helix chain 'G' and resid 388 through 400 removed outlier: 3.555A pdb=" N ALA G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 410 removed outlier: 3.596A pdb=" N ARG G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 478 through 494 removed outlier: 3.590A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 3.987A pdb=" N ILE G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 547 Processing helix chain 'G' and resid 550 through 560 Processing helix chain 'G' and resid 578 through 587 Processing helix chain 'G' and resid 614 through 618 removed outlier: 3.727A pdb=" N SER G 618 " --> pdb=" O PHE G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 664 Processing helix chain 'G' and resid 670 through 682 Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.942A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 removed outlier: 3.877A pdb=" N GLN G 771 " --> pdb=" O ASN G 768 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 831 Proline residue: G 831 - end of helix Processing helix chain 'G' and resid 832 through 837 removed outlier: 4.174A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 845 through 853 Processing helix chain 'G' and resid 894 through 898 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'B' and resid 37 through 52 removed outlier: 4.459A pdb=" N LEU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.837A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.666A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.532A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.734A pdb=" N TYR B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.590A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.607A pdb=" N GLY C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.705A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.788A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.532A pdb=" N ASP C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.579A pdb=" N HIS C 228 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.921A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.503A pdb=" N THR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 268 through 274' Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.009A pdb=" N GLU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 300 through 331 removed outlier: 3.540A pdb=" N ASP C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 386 through 401 removed outlier: 3.858A pdb=" N ARG C 390 " --> pdb=" O TRP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 Processing helix chain 'C' and resid 415 through 422 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.667A pdb=" N ASN C 449 " --> pdb=" O GLY C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 487 removed outlier: 4.330A pdb=" N LYS C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'C' and resid 563 through 572 removed outlier: 4.037A pdb=" N ALA C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 572 " --> pdb=" O HIS C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.566A pdb=" N ARG C 577 " --> pdb=" O PRO C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 removed outlier: 4.251A pdb=" N ASP C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.561A pdb=" N GLY A 34 " --> pdb=" O MET A 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 247 removed outlier: 3.702A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE H 238 " --> pdb=" O PHE H 234 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 69 removed outlier: 4.086A pdb=" N VAL J 61 " --> pdb=" O SER J 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET J 67 " --> pdb=" O ASP J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 84 through 93 removed outlier: 3.755A pdb=" N MET J 88 " --> pdb=" O THR J 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR J 92 " --> pdb=" O MET J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 137 Processing helix chain 'L' and resid 27 through 38 removed outlier: 3.860A pdb=" N MET L 32 " --> pdb=" O CYS L 28 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER L 33 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 126 through 131 Processing sheet with id=AA2, first strand: chain 'F' and resid 168 through 174 removed outlier: 6.479A pdb=" N GLY F 128 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS F 172 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE F 130 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY F 174 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU F 132 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 133 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.631A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.925A pdb=" N THR G 77 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'G' and resid 224 through 225 removed outlier: 8.002A pdb=" N ASN G 238 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN G 253 " --> pdb=" O ASN G 238 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER G 240 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE G 251 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY G 242 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 292 through 294 removed outlier: 6.177A pdb=" N VAL G 566 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL G 595 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL G 568 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE G 315 " --> pdb=" O VAL G 567 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU G 569 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE G 317 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY G 316 " --> pdb=" O TYR G 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 447 through 450 removed outlier: 3.765A pdb=" N TRP G 447 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 620 through 623 Processing sheet with id=AB3, first strand: chain 'G' and resid 704 through 705 removed outlier: 6.568A pdb=" N LEU G 704 " --> pdb=" O THR G 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 873 through 875 removed outlier: 5.729A pdb=" N ILE G 842 " --> pdb=" O GLU G 874 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG G 813 " --> pdb=" O VAL G 884 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU G 886 " --> pdb=" O ARG G 813 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA G 815 " --> pdb=" O LEU G 886 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 860 through 862 Processing sheet with id=AB6, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AB7, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.097A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AB9, first strand: chain 'B' and resid 56 through 60 removed outlier: 3.565A pdb=" N VAL B 97 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 153 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.301A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 96 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 97 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY C 79 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE C 99 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 77 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS C 101 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.603A pdb=" N VAL C 124 " --> pdb=" O ASP C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 238 removed outlier: 7.192A pdb=" N ARG C 232 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 234 " --> pdb=" O CYS C 245 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS C 245 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN C 236 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AC5, first strand: chain 'C' and resid 531 through 539 removed outlier: 3.841A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2058 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: 3.97 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8755 1.43 - 1.64: 11612 1.64 - 1.86: 203 1.86 - 2.07: 0 2.07 - 2.28: 92 Bond restraints: 20662 Sorted by residual: bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.485 1.384 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C4A FMN F 501 " pdb=" N5 FMN F 501 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' FMN F 501 " pdb=" P FMN F 501 " ideal model delta sigma weight residual 1.676 1.603 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C10 FMN F 501 " pdb=" N1 FMN F 501 " ideal model delta sigma weight residual 1.317 1.377 -0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" C10 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.443 1.385 0.058 2.00e-02 2.50e+03 8.36e+00 ... (remaining 20657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 27830 2.52 - 5.05: 194 5.05 - 7.57: 14 7.57 - 10.10: 2 10.10 - 12.62: 1 Bond angle restraints: 28041 Sorted by residual: angle pdb=" N VAL C 336 " pdb=" CA VAL C 336 " pdb=" C VAL C 336 " ideal model delta sigma weight residual 112.12 108.51 3.61 8.40e-01 1.42e+00 1.85e+01 angle pdb=" CB MET J 88 " pdb=" CG MET J 88 " pdb=" SD MET J 88 " ideal model delta sigma weight residual 112.70 125.32 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CB LYS C 200 " pdb=" CG LYS C 200 " pdb=" CD LYS C 200 " ideal model delta sigma weight residual 111.30 118.89 -7.59 2.30e+00 1.89e-01 1.09e+01 angle pdb=" C ASP C 238 " pdb=" CA ASP C 238 " pdb=" CB ASP C 238 " ideal model delta sigma weight residual 109.71 114.84 -5.13 1.83e+00 2.99e-01 7.86e+00 angle pdb=" CA LEU C 399 " pdb=" CB LEU C 399 " pdb=" CG LEU C 399 " ideal model delta sigma weight residual 116.30 126.07 -9.77 3.50e+00 8.16e-02 7.78e+00 ... (remaining 28036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 10629 17.79 - 35.57: 1252 35.57 - 53.36: 322 53.36 - 71.15: 64 71.15 - 88.93: 26 Dihedral angle restraints: 12293 sinusoidal: 4997 harmonic: 7296 Sorted by residual: dihedral pdb=" CA LEU C 237 " pdb=" C LEU C 237 " pdb=" N ASP C 238 " pdb=" CA ASP C 238 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ASP G 619 " pdb=" CB ASP G 619 " pdb=" CG ASP G 619 " pdb=" OD1 ASP G 619 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CG ARG C 364 " pdb=" CD ARG C 364 " pdb=" NE ARG C 364 " pdb=" CZ ARG C 364 " ideal model delta sinusoidal sigma weight residual -90.00 -134.17 44.17 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 12290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2045 0.037 - 0.074: 733 0.074 - 0.111: 210 0.111 - 0.148: 29 0.148 - 0.184: 1 Chirality restraints: 3018 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA ASP C 597 " pdb=" N ASP C 597 " pdb=" C ASP C 597 " pdb=" CB ASP C 597 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" C PRO C 168 " pdb=" CB PRO C 168 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 3015 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 224 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 225 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO G 764 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 117 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO I 118 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 118 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 118 " 0.020 5.00e-02 4.00e+02 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5604 2.81 - 3.33: 18849 3.33 - 3.86: 35508 3.86 - 4.38: 44826 4.38 - 4.90: 73144 Nonbonded interactions: 177931 Sorted by model distance: nonbonded pdb=" OE2 GLU G 649 " pdb="CA CA G1004 " model vdw 2.291 2.510 nonbonded pdb=" OD2 ASP G 619 " pdb="CA CA G1004 " model vdw 2.420 2.510 nonbonded pdb=" O ASP C 238 " pdb=" OD1 ASP C 238 " model vdw 2.436 3.040 nonbonded pdb=" O CYS G 233 " pdb=" O HOH G1101 " model vdw 2.517 3.040 nonbonded pdb=" O PHE B 72 " pdb=" OG1 THR B 73 " model vdw 2.525 3.040 ... (remaining 177926 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: 28.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 20699 Z= 0.153 Angle : 0.730 36.771 28137 Z= 0.266 Chirality : 0.041 0.184 3018 Planarity : 0.004 0.047 3651 Dihedral : 16.639 88.932 7621 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.61 % Allowed : 18.34 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.10 (0.17), residues: 2524 helix: 0.44 (0.17), residues: 941 sheet: -0.04 (0.33), residues: 281 loop : -0.35 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 62 TYR 0.016 0.001 TYR C 277 PHE 0.011 0.001 PHE I 91 TRP 0.008 0.001 TRP B 55 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (20662) covalent geometry : angle 0.50778 / 0.26 (28041) hydrogen bonds : bond 0.20475 / 14.29 ( 759) hydrogen bonds : angle 7.33729 / 5.16 ( 2058) metal coordination : bond 0.01223 / 0.72 ( 37) metal coordination : angle 9.00355 / 5.90 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: G 769 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.8608 (mtpt) REVERT: G 874 GLU cc_start: 0.8018 (tt0) cc_final: 0.7610 (mt-10) REVERT: B 39 MET cc_start: 0.8520 (tpp) cc_final: 0.7603 (mpp) REVERT: C 187 LYS cc_start: 0.8712 (tppt) cc_final: 0.8357 (ttmm) REVERT: C 333 MET cc_start: 0.4955 (mtm) cc_final: 0.4438 (tmt) REVERT: H 228 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: H 234 PHE cc_start: 0.8774 (t80) cc_final: 0.8474 (t80) REVERT: J 58 LEU cc_start: 0.8626 (mt) cc_final: 0.8297 (pp) REVERT: J 71 GLU cc_start: 0.7979 (tt0) cc_final: 0.7234 (tp30) outliers start: 34 outliers final: 19 residues processed: 240 average time/residue: 0.7696 time to fit residues: 205.8672 Evaluate side-chains 220 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 769 LYS Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067691 restraints weight = 38088.953| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.16 r_work: 0.2734 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20699 Z= 0.121 Angle : 0.717 36.139 28137 Z= 0.255 Chirality : 0.041 0.138 3018 Planarity : 0.004 0.048 3651 Dihedral : 5.504 75.647 2847 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 19.66 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.17), residues: 2524 helix: 0.76 (0.17), residues: 965 sheet: 0.13 (0.33), residues: 275 loop : -0.37 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 804 TYR 0.009 0.001 TYR B 136 PHE 0.013 0.001 PHE I 91 TRP 0.009 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20662) covalent geometry : angle 0.48287 / 0.25 (28041) hydrogen bonds : bond 0.03985 / 2.76 ( 759) hydrogen bonds : angle 5.38027 / 3.79 ( 2058) metal coordination : bond 0.01136 / 0.66 ( 37) metal coordination : angle 9.07881 / 5.89 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.971 Fit side-chains REVERT: E 45 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8852 (ttmt) REVERT: G 265 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8266 (p) REVERT: G 750 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.6218 (pmt170) REVERT: G 841 TYR cc_start: 0.8635 (m-80) cc_final: 0.8097 (m-80) REVERT: G 874 GLU cc_start: 0.8064 (tt0) cc_final: 0.7268 (mt-10) REVERT: B 39 MET cc_start: 0.8698 (tpp) cc_final: 0.7588 (mpp) REVERT: B 91 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7772 (mmt90) REVERT: B 192 VAL cc_start: 0.8513 (m) cc_final: 0.8260 (t) REVERT: B 219 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: C 187 LYS cc_start: 0.8440 (tppt) cc_final: 0.8125 (ttmm) REVERT: C 333 MET cc_start: 0.4762 (mtm) cc_final: 0.4448 (tmt) REVERT: H 234 PHE cc_start: 0.8660 (t80) cc_final: 0.8415 (t80) REVERT: J 58 LEU cc_start: 0.8515 (mt) cc_final: 0.8214 (pp) REVERT: J 71 GLU cc_start: 0.7834 (tt0) cc_final: 0.6989 (tp30) outliers start: 50 outliers final: 19 residues processed: 246 average time/residue: 0.7774 time to fit residues: 213.7768 Evaluate side-chains 220 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 173 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065682 restraints weight = 38152.833| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.17 r_work: 0.2715 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20699 Z= 0.174 Angle : 0.738 38.636 28137 Z= 0.264 Chirality : 0.042 0.137 3018 Planarity : 0.004 0.042 3651 Dihedral : 4.789 58.655 2826 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.88 % Allowed : 19.09 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.15 (0.17), residues: 2524 helix: 0.88 (0.17), residues: 966 sheet: 0.08 (0.33), residues: 270 loop : -0.44 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 373 TYR 0.011 0.001 TYR I 148 PHE 0.014 0.001 PHE I 91 TRP 0.010 0.001 TRP A 35 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (20662) covalent geometry : angle 0.50201 / 0.26 (28041) hydrogen bonds : bond 0.03957 / 2.72 ( 759) hydrogen bonds : angle 5.08276 / 3.58 ( 2058) metal coordination : bond 0.01555 / 0.91 ( 37) metal coordination : angle 9.27280 / 6.03 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: E 45 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8881 (ttmt) REVERT: F 95 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8659 (tp30) REVERT: G 64 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (ptt90) REVERT: G 750 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.6173 (pmt170) REVERT: G 804 ARG cc_start: 0.8734 (ptm160) cc_final: 0.8263 (ptm-80) REVERT: G 841 TYR cc_start: 0.8644 (m-80) cc_final: 0.8062 (m-80) REVERT: G 874 GLU cc_start: 0.8036 (tt0) cc_final: 0.7230 (mt-10) REVERT: B 39 MET cc_start: 0.8709 (tpp) cc_final: 0.7602 (mpp) REVERT: B 91 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7738 (mmt90) REVERT: B 119 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 192 VAL cc_start: 0.8525 (m) cc_final: 0.8284 (t) REVERT: B 219 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: C 187 LYS cc_start: 0.8436 (tppt) cc_final: 0.8123 (ttmm) REVERT: C 194 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5929 (ppp) REVERT: C 212 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7991 (t0) REVERT: C 240 GLU cc_start: 0.8340 (tt0) cc_final: 0.7978 (tp30) REVERT: C 333 MET cc_start: 0.4774 (mtm) cc_final: 0.4531 (tmt) REVERT: H 234 PHE cc_start: 0.8639 (t80) cc_final: 0.8433 (t80) REVERT: J 58 LEU cc_start: 0.8526 (mt) cc_final: 0.8240 (pp) outliers start: 61 outliers final: 25 residues processed: 243 average time/residue: 0.7461 time to fit residues: 203.8304 Evaluate side-chains 226 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 222 optimal weight: 0.0980 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 160 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.090474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068276 restraints weight = 38101.843| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.16 r_work: 0.2749 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20699 Z= 0.097 Angle : 0.690 35.037 28137 Z= 0.242 Chirality : 0.040 0.142 3018 Planarity : 0.004 0.047 3651 Dihedral : 4.441 59.162 2823 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.13 % Allowed : 19.94 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.37 (0.17), residues: 2524 helix: 1.12 (0.17), residues: 964 sheet: 0.17 (0.32), residues: 275 loop : -0.35 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 373 TYR 0.009 0.001 TYR B 136 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (20662) covalent geometry : angle 0.45955 / 0.24 (28041) hydrogen bonds : bond 0.03152 / 2.15 ( 759) hydrogen bonds : angle 4.84187 / 3.40 ( 2058) metal coordination : bond 0.00893 / 0.52 ( 37) metal coordination : angle 8.82871 / 5.77 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8685 (tp30) cc_final: 0.8373 (tp30) REVERT: E 164 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8574 (mtm-85) REVERT: G 714 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8183 (tpt170) REVERT: G 804 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8298 (ptm-80) REVERT: G 841 TYR cc_start: 0.8619 (m-80) cc_final: 0.8101 (m-80) REVERT: G 874 GLU cc_start: 0.8030 (tt0) cc_final: 0.7231 (mt-10) REVERT: B 39 MET cc_start: 0.8676 (tpp) cc_final: 0.7614 (mpp) REVERT: B 91 ARG cc_start: 0.8139 (tpp-160) cc_final: 0.7752 (mmt90) REVERT: B 166 MET cc_start: 0.7629 (tpt) cc_final: 0.7422 (tpt) REVERT: B 192 VAL cc_start: 0.8535 (m) cc_final: 0.8298 (t) REVERT: C 187 LYS cc_start: 0.8443 (tppt) cc_final: 0.8118 (ttmm) REVERT: C 194 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.5597 (ppp) REVERT: C 333 MET cc_start: 0.4820 (mtm) cc_final: 0.4546 (tmt) REVERT: H 234 PHE cc_start: 0.8653 (t80) cc_final: 0.8395 (t80) REVERT: H 238 PHE cc_start: 0.8554 (t80) cc_final: 0.8354 (t80) REVERT: J 58 LEU cc_start: 0.8478 (mt) cc_final: 0.8240 (pp) outliers start: 45 outliers final: 27 residues processed: 242 average time/residue: 0.7225 time to fit residues: 196.2979 Evaluate side-chains 229 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 93 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 171 optimal weight: 0.0070 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.068068 restraints weight = 38066.125| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.16 r_work: 0.2750 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20699 Z= 0.107 Angle : 0.693 35.958 28137 Z= 0.243 Chirality : 0.040 0.130 3018 Planarity : 0.004 0.052 3651 Dihedral : 4.217 58.615 2818 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.32 % Allowed : 20.27 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.17), residues: 2524 helix: 1.21 (0.17), residues: 964 sheet: 0.14 (0.32), residues: 280 loop : -0.32 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 373 TYR 0.009 0.001 TYR B 193 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.005 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20662) covalent geometry : angle 0.46454 / 0.24 (28041) hydrogen bonds : bond 0.03124 / 2.13 ( 759) hydrogen bonds : angle 4.74012 / 3.32 ( 2058) metal coordination : bond 0.00972 / 0.56 ( 37) metal coordination : angle 8.81699 / 5.74 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8670 (tp30) cc_final: 0.8373 (tp30) REVERT: F 95 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: G 265 CYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8208 (p) REVERT: G 714 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8173 (tpt170) REVERT: G 750 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.6203 (pmt170) REVERT: G 804 ARG cc_start: 0.8728 (ptm160) cc_final: 0.8357 (ptm-80) REVERT: G 841 TYR cc_start: 0.8628 (m-80) cc_final: 0.8115 (m-80) REVERT: G 874 GLU cc_start: 0.8045 (tt0) cc_final: 0.7232 (mt-10) REVERT: I 176 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8244 (mttp) REVERT: B 39 MET cc_start: 0.8672 (tpp) cc_final: 0.7607 (mpp) REVERT: B 51 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8219 (pttm) REVERT: B 91 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7752 (mmt90) REVERT: B 192 VAL cc_start: 0.8494 (m) cc_final: 0.8253 (t) REVERT: B 202 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8357 (mt-10) REVERT: C 187 LYS cc_start: 0.8450 (tppt) cc_final: 0.8125 (ttmm) REVERT: C 194 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5557 (ppp) REVERT: C 212 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.8013 (t0) REVERT: C 333 MET cc_start: 0.4783 (mtm) cc_final: 0.4520 (tmt) REVERT: H 234 PHE cc_start: 0.8641 (t80) cc_final: 0.8399 (t80) REVERT: H 238 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8297 (t80) REVERT: J 58 LEU cc_start: 0.8413 (mt) cc_final: 0.8197 (pp) outliers start: 49 outliers final: 25 residues processed: 239 average time/residue: 0.7291 time to fit residues: 195.7029 Evaluate side-chains 231 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 145 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 222 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN G 88 GLN G 218 ASN B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.068049 restraints weight = 37832.238| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.15 r_work: 0.2739 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20699 Z= 0.112 Angle : 0.695 36.252 28137 Z= 0.245 Chirality : 0.040 0.129 3018 Planarity : 0.004 0.054 3651 Dihedral : 4.205 58.601 2817 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.46 % Allowed : 20.51 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.52 (0.17), residues: 2524 helix: 1.27 (0.18), residues: 958 sheet: 0.16 (0.32), residues: 280 loop : -0.25 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 373 TYR 0.010 0.001 TYR B 193 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.005 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20662) covalent geometry : angle 0.46817 / 0.24 (28041) hydrogen bonds : bond 0.03102 / 2.12 ( 759) hydrogen bonds : angle 4.68692 / 3.28 ( 2058) metal coordination : bond 0.01013 / 0.59 ( 37) metal coordination : angle 8.81549 / 5.74 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.871 Fit side-chains REVERT: E 38 GLU cc_start: 0.8669 (tp30) cc_final: 0.8380 (tp30) REVERT: F 95 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: F 243 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8651 (mppt) REVERT: G 265 CYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8239 (p) REVERT: G 714 ARG cc_start: 0.8847 (mtp-110) cc_final: 0.8161 (tpt170) REVERT: G 727 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8333 (ttm-80) REVERT: G 750 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.6193 (pmt170) REVERT: G 804 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8384 (ptm-80) REVERT: G 874 GLU cc_start: 0.8037 (tt0) cc_final: 0.7224 (mt-10) REVERT: I 176 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 39 MET cc_start: 0.8668 (tpp) cc_final: 0.7624 (mpp) REVERT: B 91 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7765 (mmt90) REVERT: B 166 MET cc_start: 0.7674 (tpt) cc_final: 0.7466 (tpt) REVERT: B 192 VAL cc_start: 0.8506 (m) cc_final: 0.8263 (t) REVERT: B 202 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8333 (mt-10) REVERT: C 187 LYS cc_start: 0.8448 (tppt) cc_final: 0.8120 (ttmm) REVERT: C 194 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5534 (ppp) REVERT: C 212 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (t0) REVERT: C 240 GLU cc_start: 0.8273 (tt0) cc_final: 0.7658 (mp0) REVERT: C 333 MET cc_start: 0.4806 (mtm) cc_final: 0.4552 (tmt) REVERT: H 234 PHE cc_start: 0.8653 (t80) cc_final: 0.8412 (t80) REVERT: H 238 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8318 (t80) REVERT: J 58 LEU cc_start: 0.8406 (mt) cc_final: 0.8184 (pp) outliers start: 52 outliers final: 28 residues processed: 243 average time/residue: 0.7340 time to fit residues: 200.3716 Evaluate side-chains 232 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 469 ASN Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 160 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.088795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066509 restraints weight = 38189.302| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.15 r_work: 0.2726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20699 Z= 0.162 Angle : 0.726 38.339 28137 Z= 0.260 Chirality : 0.042 0.137 3018 Planarity : 0.004 0.058 3651 Dihedral : 4.350 56.893 2817 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.69 % Allowed : 20.37 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.41 (0.17), residues: 2524 helix: 1.15 (0.17), residues: 966 sheet: 0.07 (0.32), residues: 286 loop : -0.29 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 373 TYR 0.014 0.001 TYR C 277 PHE 0.015 0.001 PHE I 91 TRP 0.009 0.001 TRP G 653 HIS 0.005 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (20662) covalent geometry : angle 0.49700 / 0.26 (28041) hydrogen bonds : bond 0.03477 / 2.38 ( 759) hydrogen bonds : angle 4.75464 / 3.34 ( 2058) metal coordination : bond 0.01430 / 0.83 ( 37) metal coordination : angle 9.08095 / 5.89 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8687 (tp30) cc_final: 0.8409 (tp30) REVERT: F 95 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: F 243 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8662 (mppt) REVERT: G 265 CYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8328 (p) REVERT: G 714 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8185 (tpt170) REVERT: G 727 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: G 750 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.6159 (pmt170) REVERT: G 804 ARG cc_start: 0.8760 (ptm160) cc_final: 0.8377 (ptm-80) REVERT: G 841 TYR cc_start: 0.8632 (m-80) cc_final: 0.8081 (m-80) REVERT: G 874 GLU cc_start: 0.7996 (tt0) cc_final: 0.7186 (mt-10) REVERT: I 176 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8301 (mttp) REVERT: B 39 MET cc_start: 0.8649 (tpp) cc_final: 0.7619 (mpp) REVERT: B 91 ARG cc_start: 0.8169 (tpp-160) cc_final: 0.7767 (mmt90) REVERT: B 192 VAL cc_start: 0.8514 (m) cc_final: 0.8264 (t) REVERT: C 187 LYS cc_start: 0.8454 (tppt) cc_final: 0.8127 (ttmm) REVERT: C 194 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.5732 (ppp) REVERT: C 240 GLU cc_start: 0.8252 (tt0) cc_final: 0.7881 (tp30) REVERT: C 328 GLN cc_start: 0.7243 (tt0) cc_final: 0.6742 (mm-40) REVERT: H 234 PHE cc_start: 0.8685 (t80) cc_final: 0.8454 (t80) REVERT: J 58 LEU cc_start: 0.8451 (mt) cc_final: 0.8216 (pp) outliers start: 57 outliers final: 32 residues processed: 246 average time/residue: 0.7487 time to fit residues: 206.9629 Evaluate side-chains 237 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067477 restraints weight = 38006.590| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.14 r_work: 0.2727 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20699 Z= 0.128 Angle : 0.711 37.144 28137 Z= 0.253 Chirality : 0.041 0.136 3018 Planarity : 0.004 0.061 3651 Dihedral : 4.305 56.897 2817 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.22 % Allowed : 21.03 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.17), residues: 2524 helix: 1.19 (0.17), residues: 965 sheet: 0.15 (0.32), residues: 280 loop : -0.31 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 373 TYR 0.010 0.001 TYR B 193 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20662) covalent geometry : angle 0.48325 / 0.25 (28041) hydrogen bonds : bond 0.03256 / 2.22 ( 759) hydrogen bonds : angle 4.71545 / 3.31 ( 2058) metal coordination : bond 0.01168 / 0.68 ( 37) metal coordination : angle 8.95113 / 5.83 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8676 (tp30) cc_final: 0.8390 (tp30) REVERT: F 95 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: F 243 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8663 (mppt) REVERT: G 265 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8247 (p) REVERT: G 714 ARG cc_start: 0.8844 (mtp-110) cc_final: 0.8167 (tpt170) REVERT: G 750 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.6165 (pmt170) REVERT: G 804 ARG cc_start: 0.8752 (ptm160) cc_final: 0.8378 (ptm-80) REVERT: G 841 TYR cc_start: 0.8604 (m-80) cc_final: 0.8083 (m-80) REVERT: G 874 GLU cc_start: 0.8000 (tt0) cc_final: 0.7188 (mt-10) REVERT: I 176 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8291 (mttp) REVERT: B 39 MET cc_start: 0.8597 (tpp) cc_final: 0.7562 (mpp) REVERT: B 91 ARG cc_start: 0.8176 (tpp-160) cc_final: 0.7775 (mmt90) REVERT: B 192 VAL cc_start: 0.8546 (m) cc_final: 0.8290 (t) REVERT: C 187 LYS cc_start: 0.8453 (tppt) cc_final: 0.8121 (ttmm) REVERT: C 194 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.5768 (ppp) REVERT: C 240 GLU cc_start: 0.8215 (tt0) cc_final: 0.7829 (tp30) REVERT: C 328 GLN cc_start: 0.7234 (tt0) cc_final: 0.6738 (mm-40) REVERT: H 234 PHE cc_start: 0.8688 (t80) cc_final: 0.8445 (t80) REVERT: J 58 LEU cc_start: 0.8426 (mt) cc_final: 0.8209 (pp) outliers start: 47 outliers final: 31 residues processed: 243 average time/residue: 0.7517 time to fit residues: 205.0198 Evaluate side-chains 240 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 176 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 90 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 179 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 46 GLN F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067621 restraints weight = 37990.706| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.15 r_work: 0.2734 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20699 Z= 0.119 Angle : 0.709 36.602 28137 Z= 0.252 Chirality : 0.041 0.132 3018 Planarity : 0.004 0.065 3651 Dihedral : 4.269 56.712 2817 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.94 % Allowed : 21.36 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.46 (0.17), residues: 2524 helix: 1.21 (0.17), residues: 964 sheet: 0.17 (0.32), residues: 280 loop : -0.30 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 373 TYR 0.009 0.001 TYR I 148 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (20662) covalent geometry : angle 0.48459 / 0.25 (28041) hydrogen bonds : bond 0.03154 / 2.15 ( 759) hydrogen bonds : angle 4.68940 / 3.29 ( 2058) metal coordination : bond 0.01077 / 0.62 ( 37) metal coordination : angle 8.87140 / 5.78 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8679 (tp30) cc_final: 0.8397 (tp30) REVERT: F 95 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: F 243 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8659 (mppt) REVERT: G 265 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8228 (p) REVERT: G 714 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8140 (tpt170) REVERT: G 750 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.6176 (pmt170) REVERT: G 804 ARG cc_start: 0.8729 (ptm160) cc_final: 0.8382 (ptm-80) REVERT: G 841 TYR cc_start: 0.8603 (m-80) cc_final: 0.8104 (m-80) REVERT: G 874 GLU cc_start: 0.8002 (tt0) cc_final: 0.7193 (mt-10) REVERT: B 39 MET cc_start: 0.8550 (tpp) cc_final: 0.7545 (mpp) REVERT: B 91 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7781 (mmt90) REVERT: B 192 VAL cc_start: 0.8519 (m) cc_final: 0.8254 (t) REVERT: C 187 LYS cc_start: 0.8472 (tppt) cc_final: 0.8153 (ttmm) REVERT: C 194 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5833 (ppp) REVERT: C 240 GLU cc_start: 0.8222 (tt0) cc_final: 0.7840 (tp30) REVERT: C 328 GLN cc_start: 0.7236 (tt0) cc_final: 0.6935 (mm-40) REVERT: C 333 MET cc_start: 0.4662 (mtm) cc_final: 0.4348 (ptm) REVERT: H 234 PHE cc_start: 0.8663 (t80) cc_final: 0.8443 (t80) REVERT: J 58 LEU cc_start: 0.8448 (mt) cc_final: 0.8234 (pp) outliers start: 41 outliers final: 28 residues processed: 240 average time/residue: 0.7440 time to fit residues: 200.0947 Evaluate side-chains 238 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 109 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.0020 chunk 162 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 218 ASN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.068253 restraints weight = 38060.303| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.15 r_work: 0.2748 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20699 Z= 0.111 Angle : 0.711 36.112 28137 Z= 0.256 Chirality : 0.041 0.141 3018 Planarity : 0.004 0.066 3651 Dihedral : 4.244 56.883 2817 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.65 % Allowed : 21.79 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.17), residues: 2524 helix: 1.25 (0.17), residues: 963 sheet: 0.13 (0.31), residues: 291 loop : -0.28 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 373 TYR 0.009 0.001 TYR G 182 PHE 0.013 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (20662) covalent geometry : angle 0.49376 / 0.25 (28041) hydrogen bonds : bond 0.03099 / 2.11 ( 759) hydrogen bonds : angle 4.67590 / 3.27 ( 2058) metal coordination : bond 0.00989 / 0.57 ( 37) metal coordination : angle 8.78347 / 5.73 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: E 38 GLU cc_start: 0.8680 (tp30) cc_final: 0.8401 (tp30) REVERT: F 95 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: F 243 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8660 (mppt) REVERT: G 265 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8234 (p) REVERT: G 714 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8126 (tpt170) REVERT: G 750 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.6185 (pmt170) REVERT: G 804 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8394 (ptm-80) REVERT: G 874 GLU cc_start: 0.8014 (tt0) cc_final: 0.7208 (mt-10) REVERT: B 39 MET cc_start: 0.8532 (tpp) cc_final: 0.7548 (mpp) REVERT: B 91 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7786 (mmt90) REVERT: B 192 VAL cc_start: 0.8532 (m) cc_final: 0.8255 (t) REVERT: C 187 LYS cc_start: 0.8471 (tppt) cc_final: 0.8144 (ttmm) REVERT: C 240 GLU cc_start: 0.8165 (tt0) cc_final: 0.7790 (tp30) REVERT: C 328 GLN cc_start: 0.7256 (tt0) cc_final: 0.6968 (mm-40) REVERT: H 234 PHE cc_start: 0.8666 (t80) cc_final: 0.8429 (t80) REVERT: J 58 LEU cc_start: 0.8448 (mt) cc_final: 0.8238 (pp) REVERT: J 88 MET cc_start: 0.7177 (mmm) cc_final: 0.6507 (mmm) REVERT: L 32 MET cc_start: 0.6958 (pmm) cc_final: 0.6671 (pmm) outliers start: 35 outliers final: 29 residues processed: 235 average time/residue: 0.7740 time to fit residues: 203.5738 Evaluate side-chains 235 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain J residue 68 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 139 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 243 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 169 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 213 HIS G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.068104 restraints weight = 37990.619| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.14 r_work: 0.2738 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20699 Z= 0.126 Angle : 0.722 36.750 28137 Z= 0.261 Chirality : 0.041 0.158 3018 Planarity : 0.004 0.064 3651 Dihedral : 4.277 56.687 2817 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.94 % Allowed : 21.69 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.48 (0.17), residues: 2524 helix: 1.21 (0.17), residues: 966 sheet: 0.06 (0.31), residues: 298 loop : -0.25 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 373 TYR 0.010 0.001 TYR C 277 PHE 0.014 0.001 PHE I 91 TRP 0.010 0.001 TRP G 653 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20662) covalent geometry : angle 0.50456 / 0.26 (28041) hydrogen bonds : bond 0.03176 / 2.17 ( 759) hydrogen bonds : angle 4.68638 / 3.28 ( 2058) metal coordination : bond 0.01117 / 0.65 ( 37) metal coordination : angle 8.84415 / 5.75 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8374.76 seconds wall clock time: 143 minutes 28.36 seconds (8608.36 seconds total)