Starting phenix.real_space_refine on Sat Mar 7 01:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zc5_14620/03_2026/7zc5_14620.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 9 5.49 5 S 264 5.16 5 C 23878 2.51 5 N 6066 2.21 5 O 6442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36692 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4597 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 157} Chain breaks: 2 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2422 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4595 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 582} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 71.835 56.832 198.923 1.00 15.27 S ATOM 2766 SG CYS F 357 75.102 56.177 203.280 1.00 33.86 S ATOM 3087 SG CYS F 398 69.415 52.605 203.519 1.00 21.33 S ATOM 2722 SG CYS F 351 74.021 50.487 199.779 1.00 9.59 S ATOM 4079 SG CYS E 92 82.500 47.765 219.420 1.00 39.20 S ATOM 4113 SG CYS E 97 82.726 48.415 222.949 1.00 33.20 S ATOM 4391 SG CYS E 133 77.386 47.145 219.123 1.00 30.37 S ATOM 4417 SG CYS E 137 76.505 47.700 222.286 1.00 39.16 S ATOM 5501 SG CYS G 114 82.026 64.110 181.679 1.00 7.42 S ATOM 5441 SG CYS G 105 87.128 68.040 183.377 1.00 8.72 S ATOM 5461 SG CYS G 108 87.987 62.120 180.964 1.00 3.75 S ATOM 5855 SG CYS G 156 76.516 55.924 186.295 1.00 3.26 S ATOM 5836 SG CYS G 153 82.421 54.820 189.160 1.00 8.29 S ATOM 5884 SG CYS G 159 79.717 50.308 185.469 1.00 28.24 S ATOM 6228 SG CYS G 203 81.620 55.616 182.555 1.00 11.64 S ATOM 6453 SG CYS G 230 78.732 48.229 161.051 1.00 22.69 S ATOM 6738 SG CYS G 265 78.832 44.185 166.188 1.00 11.99 S ATOM 6501 SG CYS G 237 73.443 47.583 164.132 1.00 16.95 S ATOM 6477 SG CYS G 233 75.964 42.272 161.028 1.00 21.47 S ATOM 4902 SG CYS G 36 69.961 56.444 188.890 1.00 27.17 S ATOM 4978 SG CYS G 47 71.486 59.801 189.586 1.00 0.58 S ATOM 5004 SG CYS G 50 65.718 61.357 189.396 1.00 10.56 S ATOM 5153 SG CYS G 69 65.332 57.691 188.799 1.00 11.74 S ATOM 16888 SG CYS B 129 91.517 92.756 159.117 1.00 32.65 S ATOM 16524 SG CYS B 64 96.606 96.659 160.839 1.00 78.96 S ATOM 16518 SG CYS B 63 90.871 98.355 162.837 1.00 71.20 S ATOM 17105 SG CYS B 158 93.408 92.573 164.821 1.00 46.15 S ATOM 18149 SG CYS I 102 92.212 86.254 170.609 1.00 0.58 S ATOM 18124 SG CYS I 99 97.666 85.313 166.876 1.00 5.18 S ATOM 18167 SG CYS I 105 96.350 81.721 172.184 1.00 7.10 S ATOM 17882 SG CYS I 70 92.528 81.135 166.973 1.00 0.78 S ATOM 18196 SG CYS I 109 97.489 75.992 178.170 1.00 4.79 S ATOM 17859 SG CYS I 66 95.529 75.391 172.066 1.00 8.01 S ATOM 17819 SG CYS I 60 99.805 71.150 174.161 1.00 6.84 S ATOM 17837 SG CYS I 63 93.498 71.419 176.629 1.00 8.67 S Time building chain proxies: 8.41, per 1000 atoms: 0.23 Number of scatterers: 36692 At special positions: 0 Unit cell: (157.94, 209.88, 252.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 264 16.00 P 9 15.00 O 6442 8.00 N 6066 7.00 C 23878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 24 sheets defined 61.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.694A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.663A 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 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.603A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 301 through 307 removed outlier: 4.144A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 316 removed outlier: 3.528A pdb=" N ILE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 390 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.669A pdb=" N GLY F 403 " --> pdb=" O ALA F 399 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 422 removed outlier: 4.115A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 27 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 63 removed outlier: 3.887A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 101 through 114 removed outlier: 4.068A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.555A pdb=" N GLY E 140 " --> pdb=" O CYS E 137 " (cutoff:3.500A) 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 '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 removed outlier: 3.524A pdb=" N GLY G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 153 Processing helix chain 'G' and resid 157 through 166 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: 4.128A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 265 through 271 Processing helix chain 'G' and resid 296 through 311 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'G' and resid 383 through 388 Processing helix chain 'G' and resid 388 through 410 removed outlier: 3.808A pdb=" N ALA G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 424 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 478 through 495 removed outlier: 3.509A pdb=" N ALA G 495 " --> pdb=" O ALA G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 3.840A pdb=" N ILE G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG G 525 " --> pdb=" O ALA G 521 " (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 589 Processing helix chain 'G' and resid 600 through 604 removed outlier: 3.612A pdb=" N MET G 603 " --> pdb=" O THR G 600 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 600 through 604' Processing helix chain 'G' and resid 649 through 663 Processing helix chain 'G' and resid 670 through 682 Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.961A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 removed outlier: 3.574A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN G 771 " --> pdb=" O ASN G 768 " (cutoff:3.500A) Processing helix chain 'G' and resid 824 through 830 Processing helix chain 'G' and resid 832 through 837 removed outlier: 4.116A 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 'C' and resid 23 through 34 removed outlier: 3.674A pdb=" N GLY C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 3.503A pdb=" N LYS C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 280 through 296 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 300 through 327 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 386 through 400 removed outlier: 4.270A 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 432 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 462 through 487 removed outlier: 3.547A pdb=" N ASN C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 511 Processing helix chain 'C' and resid 511 through 523 Processing helix chain 'C' and resid 563 through 571 removed outlier: 4.099A pdb=" N ALA C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.506A pdb=" N ILE C 576 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 591 Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.049A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'H' and resid 5 through 40 Processing helix chain 'H' and resid 56 through 70 Processing helix chain 'H' and resid 79 through 98 Proline residue: H 87 - end of helix removed outlier: 5.043A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.421A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 172 removed outlier: 5.043A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 183 Processing helix chain 'H' and resid 192 through 207 removed outlier: 3.536A pdb=" N CYS H 207 " --> pdb=" O GLY H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 219 removed outlier: 3.769A pdb=" N GLU H 218 " --> pdb=" O PRO H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 257 Processing helix chain 'H' and resid 266 through 288 Processing helix chain 'H' and resid 293 through 323 removed outlier: 5.496A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 6 through 37 Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.843A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 3.501A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 22 Proline residue: L 11 - end of helix removed outlier: 3.766A pdb=" N ARG L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 55 Processing helix chain 'L' and resid 82 through 107 Processing helix chain 'L' and resid 112 through 132 Processing helix chain 'L' and resid 135 through 155 Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.610A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 208 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 212 through 230 Processing helix chain 'L' and resid 240 through 244 removed outlier: 3.997A pdb=" N MET L 243 " --> pdb=" O ALA L 240 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 244 " --> pdb=" O ASP L 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 244' Processing helix chain 'L' and resid 246 through 255 Processing helix chain 'L' and resid 260 through 269 Processing helix chain 'L' and resid 269 through 275 removed outlier: 3.813A pdb=" N MET L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 299 removed outlier: 3.642A pdb=" N LEU L 299 " --> pdb=" O GLY L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 356 Processing helix chain 'L' and resid 372 through 387 Processing helix chain 'L' and resid 393 through 409 removed outlier: 3.871A pdb=" N PHE L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 437 Processing helix chain 'L' and resid 454 through 464 Processing helix chain 'L' and resid 465 through 471 removed outlier: 3.668A pdb=" N ALA L 469 " --> pdb=" O THR L 465 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE L 471 " --> pdb=" O VAL L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 486 through 513 Processing helix chain 'L' and resid 516 through 525 Processing helix chain 'L' and resid 525 through 536 Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 540 through 560 removed outlier: 5.220A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 563 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 590 through 613 Processing helix chain 'M' and resid 2 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 24 Processing helix chain 'M' and resid 27 through 51 removed outlier: 4.286A pdb=" N GLY M 51 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 105 Processing helix chain 'M' and resid 112 through 133 Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.586A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 158 Processing helix chain 'M' and resid 164 through 200 removed outlier: 3.903A pdb=" N ILE M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 216 through 235 removed outlier: 3.808A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 250 removed outlier: 4.416A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 262 removed outlier: 3.512A pdb=" N LEU M 259 " --> pdb=" O GLY M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 275 removed outlier: 4.335A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 308 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.676A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 Processing helix chain 'M' and resid 383 through 397 Processing helix chain 'M' and resid 401 through 418 removed outlier: 3.889A pdb=" N VAL M 405 " --> pdb=" O THR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 445 removed outlier: 3.630A pdb=" N THR M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE M 445 " --> pdb=" O HIS M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 503 removed outlier: 4.664A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN M 502 " --> pdb=" O GLN M 498 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER M 503 " --> pdb=" O TRP M 499 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 10 Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 58 Processing helix chain 'N' and resid 70 through 97 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 121 Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.562A pdb=" N GLY N 144 " --> pdb=" O PHE N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 181 Processing helix chain 'N' and resid 185 through 189 removed outlier: 3.670A pdb=" N LEU N 189 " --> pdb=" O PHE N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 218 Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 261 removed outlier: 4.364A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.904A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 266 through 288 Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.757A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 Processing helix chain 'N' and resid 364 through 368 removed outlier: 3.581A pdb=" N TRP N 367 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 384 Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.569A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 432 Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 480 Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.582A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.548A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 58 Processing helix chain 'J' and resid 62 through 75 Processing helix chain 'J' and resid 85 through 88 Processing helix chain 'J' and resid 89 through 112 removed outlier: 3.763A pdb=" N TRP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 160 Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160 removed outlier: 5.888A pdb=" N PHE F 165 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY F 128 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N HIS F 172 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE F 130 " --> pdb=" O HIS F 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 262 through 265 removed outlier: 7.244A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.682A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.979A pdb=" N THR G 5 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE G 79 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS G 7 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 4.443A 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: 6.435A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 291 through 294 removed outlier: 6.475A pdb=" N VAL G 566 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL G 595 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 568 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 315 " --> pdb=" O VAL G 567 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU G 569 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE G 317 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.041A 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: 6.306A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR G 532 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE G 500 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE G 534 " --> pdb=" O ILE G 500 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER G 502 " --> pdb=" O ILE G 534 " (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: 6.512A 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 812 through 817 removed outlier: 5.823A pdb=" N ILE G 842 " --> pdb=" O GLU G 874 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER G 863 " --> pdb=" O ASP G 904 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.310A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER C 97 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY C 79 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 99 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 77 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS C 101 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'C' and resid 215 through 220 removed outlier: 3.665A pdb=" N ILE C 233 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AB9, first strand: chain 'C' and resid 532 through 539 removed outlier: 3.597A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AC2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.681A pdb=" N ALA B 99 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.769A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 60 through 70 removed outlier: 7.052A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR L 66 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE L 75 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N MET L 68 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE L 73 " --> pdb=" O MET L 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.849A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 2129 hydrogen bonds defined for protein. 6180 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: 8.34 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15629 1.42 - 1.64: 21483 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37607 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.380 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.604 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.367 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.376 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O13 3PE J 301 " pdb=" P 3PE J 301 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.28e+00 ... (remaining 37602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 50722 4.27 - 8.54: 274 8.54 - 12.81: 27 12.81 - 17.07: 6 17.07 - 21.34: 1 Bond angle restraints: 51030 Sorted by residual: angle pdb=" CA PRO H 6 " pdb=" N PRO H 6 " pdb=" CD PRO H 6 " ideal model delta sigma weight residual 112.00 99.42 12.58 1.40e+00 5.10e-01 8.07e+01 angle pdb=" CB MET G 67 " pdb=" CG MET G 67 " pdb=" SD MET G 67 " ideal model delta sigma weight residual 112.70 91.36 21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 96.82 12.99 2.21e+00 2.05e-01 3.45e+01 angle pdb=" CB MET L 214 " pdb=" CG MET L 214 " pdb=" SD MET L 214 " ideal model delta sigma weight residual 112.70 128.78 -16.08 3.00e+00 1.11e-01 2.87e+01 angle pdb=" CB MET N 379 " pdb=" CG MET N 379 " pdb=" SD MET N 379 " ideal model delta sigma weight residual 112.70 128.23 -15.53 3.00e+00 1.11e-01 2.68e+01 ... (remaining 51025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 20767 25.53 - 51.07: 1183 51.07 - 76.60: 170 76.60 - 102.13: 22 102.13 - 127.67: 2 Dihedral angle restraints: 22144 sinusoidal: 8880 harmonic: 13264 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.06 44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual -180.00 -145.53 -34.47 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.67 34.33 0 5.00e+00 4.00e-02 4.71e+01 ... (remaining 22141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5680 4.238 - 8.476: 0 8.476 - 12.714: 0 12.714 - 16.953: 0 16.953 - 21.191: 28 Chirality restraints: 5708 Sorted by residual: chirality pdb="FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5705 not shown) Planarity restraints: 6380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C VAL N 63 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.028 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 5 " -0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO H 6 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO H 6 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 6 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 210 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO H 211 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.036 5.00e-02 4.00e+02 ... (remaining 6377 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5023 2.75 - 3.29: 34929 3.29 - 3.83: 66353 3.83 - 4.36: 80171 4.36 - 4.90: 136269 Nonbonded interactions: 322745 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.255 3.040 nonbonded pdb=" O SER K 96 " pdb=" OG SER K 96 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR G 364 " pdb=" OE1 GLU G 370 " model vdw 2.262 3.040 nonbonded pdb=" O GLY L 421 " pdb=" OG1 THR L 425 " model vdw 2.264 3.040 ... (remaining 322740 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.000 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 37643 Z= 0.296 Angle : 0.878 21.342 51123 Z= 0.437 Chirality : 1.478 21.191 5708 Planarity : 0.007 0.106 6380 Dihedral : 15.708 127.666 13660 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 1.96 % Allowed : 16.62 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.09 % 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: -0.62 (0.11), residues: 4601 helix: 0.03 (0.09), residues: 2689 sheet: -0.79 (0.28), residues: 307 loop : -0.89 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 93 TYR 0.037 0.003 TYR C 277 PHE 0.038 0.002 PHE L 341 TRP 0.021 0.002 TRP H 107 HIS 0.007 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00693 (37607) covalent geometry : angle 0.85923 (51030) hydrogen bonds : bond 0.13218 ( 2127) hydrogen bonds : angle 6.08161 ( 6180) metal coordination : bond 0.06152 ( 36) metal coordination : angle 4.30481 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 412 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: G 670 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: G 855 ASN cc_start: 0.8694 (p0) cc_final: 0.8098 (p0) REVERT: G 904 ASP cc_start: 0.8102 (m-30) cc_final: 0.7509 (p0) REVERT: C 189 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6890 (tttt) REVERT: B 219 GLU cc_start: 0.8527 (pm20) cc_final: 0.8204 (pm20) REVERT: L 101 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7424 (tpt) REVERT: L 236 GLN cc_start: 0.8979 (pm20) cc_final: 0.8538 (pm20) REVERT: L 407 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: M 291 MET cc_start: 0.8789 (mtm) cc_final: 0.8425 (mtm) REVERT: J 89 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8883 (ptpp) outliers start: 74 outliers final: 50 residues processed: 467 average time/residue: 0.7041 time to fit residues: 393.3949 Evaluate side-chains 443 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 390 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 459 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 106 GLN G 655 HIS C 409 GLN M 119 ASN M 198 ASN N 37 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071449 restraints weight = 60162.301| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.39 r_work: 0.2904 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37643 Z= 0.406 Angle : 2.521 51.012 51123 Z= 1.451 Chirality : 0.445 6.451 5708 Planarity : 0.005 0.074 6380 Dihedral : 8.600 125.407 5555 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 2.99 % Allowed : 15.38 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4601 helix: 0.99 (0.10), residues: 2671 sheet: -0.75 (0.29), residues: 299 loop : -0.58 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 378 TYR 0.022 0.001 TYR L 428 PHE 0.028 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01177 (37607) covalent geometry : angle 2.20189 (51030) hydrogen bonds : bond 0.04949 ( 2127) hydrogen bonds : angle 4.90295 ( 6180) metal coordination : bond 0.04786 ( 36) metal coordination : angle 28.88652 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 414 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 64 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.8175 (ttp-170) REVERT: G 416 GLN cc_start: 0.8247 (tt0) cc_final: 0.8010 (mt0) REVERT: G 664 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8365 (mtp-110) REVERT: G 904 ASP cc_start: 0.7731 (m-30) cc_final: 0.7508 (p0) REVERT: C 187 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7941 (mptm) REVERT: C 262 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6885 (mmm160) REVERT: B 2 ASP cc_start: 0.8018 (m-30) cc_final: 0.7634 (p0) REVERT: B 68 MET cc_start: 0.7016 (ptm) cc_final: 0.6791 (ptp) REVERT: B 183 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8538 (mm) REVERT: B 219 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: I 153 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7678 (mmm) REVERT: H 68 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7558 (t80) REVERT: H 107 TRP cc_start: 0.7232 (m-90) cc_final: 0.6762 (m-90) REVERT: H 232 MET cc_start: 0.7919 (tpp) cc_final: 0.7718 (tpp) REVERT: L 101 MET cc_start: 0.8039 (mtp) cc_final: 0.7205 (tpt) REVERT: L 236 GLN cc_start: 0.8510 (pm20) cc_final: 0.8170 (pm20) REVERT: L 490 MET cc_start: 0.6259 (tpt) cc_final: 0.5956 (tpt) REVERT: L 569 MET cc_start: 0.7637 (mmm) cc_final: 0.7242 (mmm) REVERT: M 115 PHE cc_start: 0.7202 (t80) cc_final: 0.6986 (t80) REVERT: M 150 MET cc_start: 0.8268 (ttm) cc_final: 0.8005 (mtt) REVERT: M 291 MET cc_start: 0.8538 (mtm) cc_final: 0.8247 (mtm) REVERT: M 374 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7006 (ptt) REVERT: M 408 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: N 36 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7464 (tm) REVERT: N 74 MET cc_start: 0.7675 (mtm) cc_final: 0.7298 (mtp) REVERT: N 485 MET cc_start: 0.5444 (mpt) cc_final: 0.4829 (mpp) REVERT: K 75 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7993 (tp) outliers start: 113 outliers final: 43 residues processed: 486 average time/residue: 0.7045 time to fit residues: 412.4043 Evaluate side-chains 445 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 392 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 438 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 312 optimal weight: 8.9990 chunk 360 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 237 GLN F 386 GLN B 196 ASN H 226 HIS L 55 ASN M 119 ASN K 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068224 restraints weight = 59797.219| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.41 r_work: 0.2827 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.258 37643 Z= 0.458 Angle : 2.538 50.582 51123 Z= 1.458 Chirality : 0.453 6.642 5708 Planarity : 0.005 0.071 6380 Dihedral : 8.459 124.580 5499 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 3.51 % Allowed : 15.14 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4601 helix: 1.11 (0.10), residues: 2683 sheet: -0.64 (0.30), residues: 305 loop : -0.47 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 93 TYR 0.022 0.002 TYR M 207 PHE 0.028 0.002 PHE I 101 TRP 0.021 0.002 TRP L 143 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.01262 (37607) covalent geometry : angle 2.22270 (51030) hydrogen bonds : bond 0.05623 ( 2127) hydrogen bonds : angle 4.92957 ( 6180) metal coordination : bond 0.06211 ( 36) metal coordination : angle 28.78999 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 398 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: E 82 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: G 64 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8006 (ptt-90) REVERT: G 750 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.7559 (ppt-90) REVERT: G 858 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9060 (p) REVERT: G 904 ASP cc_start: 0.7870 (m-30) cc_final: 0.7595 (p0) REVERT: C 127 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: C 262 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7197 (mmm160) REVERT: B 2 ASP cc_start: 0.8047 (m-30) cc_final: 0.7774 (p0) REVERT: B 91 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7390 (mmp80) REVERT: B 183 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 194 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6779 (mpp80) REVERT: B 219 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: I 153 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: H 107 TRP cc_start: 0.7235 (m-90) cc_final: 0.6788 (m-90) REVERT: H 109 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6881 (t) REVERT: H 114 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7714 (pt) REVERT: H 170 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: H 232 MET cc_start: 0.8117 (tpp) cc_final: 0.7803 (tpp) REVERT: H 296 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6364 (mt0) REVERT: L 101 MET cc_start: 0.8067 (mtp) cc_final: 0.7204 (tpt) REVERT: L 185 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7318 (mp) REVERT: L 311 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7513 (p) REVERT: M 291 MET cc_start: 0.8576 (mtm) cc_final: 0.8181 (mtm) REVERT: M 398 MET cc_start: 0.8000 (tpp) cc_final: 0.7602 (tpp) REVERT: M 408 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: N 36 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7381 (tm) REVERT: N 64 THR cc_start: 0.8033 (m) cc_final: 0.7267 (m) REVERT: N 74 MET cc_start: 0.7654 (mtm) cc_final: 0.7284 (mtp) REVERT: K 75 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8185 (tp) REVERT: K 88 GLN cc_start: 0.8431 (mp10) cc_final: 0.7946 (mp10) REVERT: J 18 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7447 (mmp-170) REVERT: J 86 GLN cc_start: 0.8075 (mp10) cc_final: 0.7591 (mp10) REVERT: J 89 LYS cc_start: 0.9060 (mttp) cc_final: 0.8800 (ptpp) outliers start: 133 outliers final: 52 residues processed: 482 average time/residue: 0.7176 time to fit residues: 412.7740 Evaluate side-chains 450 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 378 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 55 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 408 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN M 113 GLN M 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070110 restraints weight = 59562.830| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.38 r_work: 0.2877 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37643 Z= 0.401 Angle : 2.519 50.564 51123 Z= 1.450 Chirality : 0.448 6.498 5708 Planarity : 0.005 0.071 6380 Dihedral : 8.230 127.397 5495 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 3.20 % Allowed : 15.88 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4601 helix: 1.40 (0.10), residues: 2677 sheet: -0.69 (0.29), residues: 300 loop : -0.41 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 93 TYR 0.022 0.002 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01156 (37607) covalent geometry : angle 2.20004 (51030) hydrogen bonds : bond 0.04756 ( 2127) hydrogen bonds : angle 4.72426 ( 6180) metal coordination : bond 0.04192 ( 36) metal coordination : angle 28.87225 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 393 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7992 (mttp) REVERT: F 182 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: F 255 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8106 (mmm160) REVERT: G 64 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8233 (ttp-170) REVERT: G 416 GLN cc_start: 0.8293 (tt0) cc_final: 0.8058 (mt0) REVERT: G 664 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8304 (mtp-110) REVERT: G 904 ASP cc_start: 0.7836 (m-30) cc_final: 0.7603 (p0) REVERT: C 127 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: C 262 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7033 (mmm160) REVERT: C 576 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8706 (pp) REVERT: B 2 ASP cc_start: 0.8001 (m-30) cc_final: 0.7730 (p0) REVERT: B 91 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7665 (mmp80) REVERT: B 183 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8530 (mm) REVERT: B 194 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6698 (mpp80) REVERT: B 219 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: I 153 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: H 60 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7341 (tm) REVERT: H 107 TRP cc_start: 0.7177 (m-90) cc_final: 0.6732 (m-90) REVERT: H 109 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6772 (t) REVERT: H 114 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7582 (pt) REVERT: H 232 MET cc_start: 0.8078 (tpp) cc_final: 0.7832 (tpp) REVERT: H 285 ILE cc_start: 0.8443 (pt) cc_final: 0.8223 (pp) REVERT: L 101 MET cc_start: 0.8083 (mtp) cc_final: 0.7341 (tpt) REVERT: L 490 MET cc_start: 0.6457 (tpt) cc_final: 0.6126 (tpt) REVERT: L 533 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8347 (p) REVERT: L 568 MET cc_start: 0.7328 (tpp) cc_final: 0.6665 (tmm) REVERT: M 291 MET cc_start: 0.8551 (mtm) cc_final: 0.8170 (mtm) REVERT: M 398 MET cc_start: 0.7832 (tpp) cc_final: 0.7407 (tpp) REVERT: M 408 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: N 36 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7376 (tm) REVERT: N 74 MET cc_start: 0.7578 (mtm) cc_final: 0.7208 (mtp) REVERT: K 75 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (tp) REVERT: J 69 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7820 (t80) outliers start: 121 outliers final: 56 residues processed: 471 average time/residue: 0.6997 time to fit residues: 394.5708 Evaluate side-chains 453 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 378 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 209 optimal weight: 7.9990 chunk 457 optimal weight: 5.9990 chunk 387 optimal weight: 20.0000 chunk 370 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN M 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069816 restraints weight = 59420.169| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.36 r_work: 0.2869 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37643 Z= 0.408 Angle : 2.522 50.560 51123 Z= 1.451 Chirality : 0.448 6.516 5708 Planarity : 0.005 0.070 6380 Dihedral : 8.135 127.592 5493 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 3.30 % Allowed : 16.09 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 4601 helix: 1.47 (0.10), residues: 2680 sheet: -0.59 (0.30), residues: 304 loop : -0.40 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 378 TYR 0.021 0.002 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01169 (37607) covalent geometry : angle 2.20354 (51030) hydrogen bonds : bond 0.04816 ( 2127) hydrogen bonds : angle 4.69153 ( 6180) metal coordination : bond 0.04398 ( 36) metal coordination : angle 28.84516 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 395 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8038 (mttp) REVERT: F 182 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: F 255 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8151 (mmm160) REVERT: G 64 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8205 (ttp-170) REVERT: G 252 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: G 416 GLN cc_start: 0.8313 (tt0) cc_final: 0.8069 (mt0) REVERT: G 664 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8235 (mtp-110) REVERT: G 806 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7925 (tp40) REVERT: G 834 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7895 (mp-120) REVERT: G 904 ASP cc_start: 0.7865 (m-30) cc_final: 0.7632 (p0) REVERT: C 127 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: C 262 ARG cc_start: 0.7422 (mtp180) cc_final: 0.7104 (mmm160) REVERT: C 576 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8712 (pp) REVERT: C 595 MET cc_start: 0.9155 (mmm) cc_final: 0.8925 (mmm) REVERT: B 2 ASP cc_start: 0.7992 (m-30) cc_final: 0.7736 (p0) REVERT: B 180 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7499 (ptm160) REVERT: B 183 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8534 (mm) REVERT: B 194 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6680 (mpp80) REVERT: B 219 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: I 153 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7620 (mmm) REVERT: H 32 MET cc_start: 0.8186 (mtp) cc_final: 0.7947 (mtp) REVERT: H 60 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7398 (tm) REVERT: H 107 TRP cc_start: 0.7197 (m-90) cc_final: 0.6802 (m-90) REVERT: H 114 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (pt) REVERT: H 232 MET cc_start: 0.8058 (tpp) cc_final: 0.7818 (tpp) REVERT: H 285 ILE cc_start: 0.8416 (pt) cc_final: 0.8203 (pp) REVERT: L 101 MET cc_start: 0.8064 (mtp) cc_final: 0.7313 (tpt) REVERT: L 568 MET cc_start: 0.7274 (tpp) cc_final: 0.6673 (tmm) REVERT: M 291 MET cc_start: 0.8563 (mtm) cc_final: 0.8199 (mtm) REVERT: M 381 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: M 398 MET cc_start: 0.7829 (tpp) cc_final: 0.7436 (tpp) REVERT: M 408 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: N 36 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7368 (tm) REVERT: N 74 MET cc_start: 0.7597 (mtm) cc_final: 0.7249 (mtp) REVERT: K 75 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8099 (tp) REVERT: J 18 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7412 (mmp-170) REVERT: J 69 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7861 (t80) outliers start: 125 outliers final: 63 residues processed: 475 average time/residue: 0.7167 time to fit residues: 406.6714 Evaluate side-chains 464 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 381 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 178 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 396 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 364 optimal weight: 2.9990 chunk 355 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN H 210 HIS M 113 GLN M 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069562 restraints weight = 59559.464| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.39 r_work: 0.2861 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37643 Z= 0.410 Angle : 2.524 50.584 51123 Z= 1.451 Chirality : 0.449 6.517 5708 Planarity : 0.005 0.070 6380 Dihedral : 8.052 127.744 5493 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 3.30 % Allowed : 16.57 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4601 helix: 1.51 (0.10), residues: 2680 sheet: -0.60 (0.30), residues: 304 loop : -0.40 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 287 TYR 0.023 0.002 TYR J 109 PHE 0.027 0.002 PHE L 341 TRP 0.023 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01173 (37607) covalent geometry : angle 2.20519 (51030) hydrogen bonds : bond 0.04832 ( 2127) hydrogen bonds : angle 4.67808 ( 6180) metal coordination : bond 0.04399 ( 36) metal coordination : angle 28.85382 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 394 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8033 (mttp) REVERT: F 158 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8833 (mmtp) REVERT: F 182 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: F 255 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (mmm160) REVERT: E 82 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8472 (mt0) REVERT: G 64 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8168 (ttp-170) REVERT: G 252 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: G 416 GLN cc_start: 0.8331 (tt0) cc_final: 0.8074 (mt0) REVERT: G 528 ASP cc_start: 0.8371 (t0) cc_final: 0.7874 (t0) REVERT: G 664 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8208 (mtp-110) REVERT: G 806 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: G 834 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7908 (mp-120) REVERT: G 858 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9057 (p) REVERT: C 127 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: C 576 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8717 (pp) REVERT: B 2 ASP cc_start: 0.7999 (m-30) cc_final: 0.7729 (p0) REVERT: B 91 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7669 (mmp80) REVERT: B 180 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7482 (ptm160) REVERT: B 183 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8528 (mm) REVERT: B 194 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6676 (mpp80) REVERT: B 219 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: I 153 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: H 60 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7409 (tm) REVERT: H 107 TRP cc_start: 0.7205 (m-90) cc_final: 0.6805 (m-90) REVERT: H 114 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7566 (pt) REVERT: H 232 MET cc_start: 0.8072 (tpp) cc_final: 0.7760 (tpp) REVERT: H 285 ILE cc_start: 0.8410 (pt) cc_final: 0.8194 (pp) REVERT: L 101 MET cc_start: 0.8069 (mtp) cc_final: 0.7315 (tpt) REVERT: L 568 MET cc_start: 0.7310 (tpp) cc_final: 0.6602 (tmm) REVERT: M 291 MET cc_start: 0.8566 (mtm) cc_final: 0.8201 (mtm) REVERT: M 381 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: M 398 MET cc_start: 0.7868 (tpp) cc_final: 0.7485 (tpp) REVERT: M 408 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: N 36 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7403 (tm) REVERT: N 74 MET cc_start: 0.7567 (mtm) cc_final: 0.7220 (mtp) REVERT: N 154 GLU cc_start: 0.7409 (tp30) cc_final: 0.7122 (mm-30) REVERT: K 75 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8103 (tp) REVERT: J 18 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7471 (mmp-170) REVERT: J 69 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7870 (t80) outliers start: 125 outliers final: 63 residues processed: 475 average time/residue: 0.7324 time to fit residues: 414.8619 Evaluate side-chains 463 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 376 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 312 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 440 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 404 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN H 210 HIS M 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069796 restraints weight = 59402.233| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.38 r_work: 0.2870 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37643 Z= 0.410 Angle : 2.525 50.581 51123 Z= 1.452 Chirality : 0.449 6.517 5708 Planarity : 0.005 0.070 6380 Dihedral : 8.040 127.064 5493 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.12 % Allowed : 17.12 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 4601 helix: 1.51 (0.10), residues: 2681 sheet: -0.63 (0.30), residues: 303 loop : -0.41 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 26 TYR 0.021 0.002 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.021 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01174 (37607) covalent geometry : angle 2.20714 (51030) hydrogen bonds : bond 0.04822 ( 2127) hydrogen bonds : angle 4.68136 ( 6180) metal coordination : bond 0.04363 ( 36) metal coordination : angle 28.85538 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 396 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8040 (mttp) REVERT: F 158 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8826 (mmtp) REVERT: F 182 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: F 255 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (mmm160) REVERT: E 82 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: G 64 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8168 (ttp-170) REVERT: G 252 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: G 416 GLN cc_start: 0.8307 (tt0) cc_final: 0.8057 (mt0) REVERT: G 664 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8219 (mtp-110) REVERT: G 806 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: G 834 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7917 (mp-120) REVERT: G 858 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9099 (p) REVERT: C 127 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: C 200 LYS cc_start: 0.8545 (tppt) cc_final: 0.8329 (tppp) REVERT: C 228 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6560 (p90) REVERT: C 576 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 2 ASP cc_start: 0.7984 (m-30) cc_final: 0.7742 (p0) REVERT: B 39 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7248 (pmm) REVERT: B 180 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7546 (ptm160) REVERT: B 183 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8528 (mm) REVERT: B 194 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6686 (mpp80) REVERT: B 219 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: I 153 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7620 (mmm) REVERT: H 32 MET cc_start: 0.8287 (mtp) cc_final: 0.8039 (mtp) REVERT: H 60 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7423 (tm) REVERT: H 107 TRP cc_start: 0.7207 (m-90) cc_final: 0.6799 (m-90) REVERT: H 114 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7554 (pt) REVERT: H 232 MET cc_start: 0.7949 (tpp) cc_final: 0.7724 (tpp) REVERT: H 285 ILE cc_start: 0.8432 (pt) cc_final: 0.8229 (pp) REVERT: L 101 MET cc_start: 0.8089 (mtp) cc_final: 0.7308 (tpt) REVERT: L 236 GLN cc_start: 0.8517 (pm20) cc_final: 0.8237 (pm20) REVERT: L 319 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6741 (mmm) REVERT: L 568 MET cc_start: 0.7289 (tpp) cc_final: 0.6571 (tmm) REVERT: M 291 MET cc_start: 0.8590 (mtm) cc_final: 0.8221 (mtm) REVERT: M 381 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7745 (mtt) REVERT: M 398 MET cc_start: 0.7843 (tpp) cc_final: 0.7481 (tpp) REVERT: M 408 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: N 36 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7486 (tm) REVERT: N 74 MET cc_start: 0.7576 (mtm) cc_final: 0.7230 (mtp) REVERT: K 75 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8087 (tp) REVERT: K 86 ARG cc_start: 0.8296 (mtt90) cc_final: 0.8013 (mmt180) REVERT: K 88 GLN cc_start: 0.8413 (mp10) cc_final: 0.8149 (mm-40) REVERT: J 69 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7878 (t80) REVERT: J 88 LEU cc_start: 0.7298 (mm) cc_final: 0.6914 (mm) outliers start: 118 outliers final: 64 residues processed: 471 average time/residue: 0.7160 time to fit residues: 401.8109 Evaluate side-chains 473 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 384 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 71 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 431 optimal weight: 2.9990 chunk 406 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 413 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN M 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069750 restraints weight = 59353.683| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.39 r_work: 0.2866 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37643 Z= 0.408 Angle : 2.526 50.615 51123 Z= 1.452 Chirality : 0.448 6.506 5708 Planarity : 0.004 0.071 6380 Dihedral : 8.009 126.785 5493 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.01 % Allowed : 17.68 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4601 helix: 1.54 (0.10), residues: 2679 sheet: -0.64 (0.30), residues: 303 loop : -0.39 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 287 TYR 0.021 0.002 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.024 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01170 (37607) covalent geometry : angle 2.20747 (51030) hydrogen bonds : bond 0.04782 ( 2127) hydrogen bonds : angle 4.66399 ( 6180) metal coordination : bond 0.04297 ( 36) metal coordination : angle 28.86156 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 392 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 158 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8839 (mmtp) REVERT: F 182 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: F 255 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8153 (mmm160) REVERT: F 302 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 82 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: G 64 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8211 (ttp-170) REVERT: G 252 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: G 416 GLN cc_start: 0.8307 (tt0) cc_final: 0.8049 (mt0) REVERT: G 528 ASP cc_start: 0.8353 (t0) cc_final: 0.8082 (t0) REVERT: G 664 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8238 (mtp-110) REVERT: G 806 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (tp40) REVERT: G 834 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7918 (mp-120) REVERT: C 127 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: C 228 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6571 (p90) REVERT: C 576 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 2 ASP cc_start: 0.7986 (m-30) cc_final: 0.7706 (p0) REVERT: B 39 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7423 (pmm) REVERT: B 91 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7670 (mmp80) REVERT: B 178 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8714 (mtmm) REVERT: B 180 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7556 (ptm160) REVERT: B 194 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6669 (mpp80) REVERT: B 219 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: I 153 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: H 60 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7471 (tm) REVERT: H 107 TRP cc_start: 0.7251 (m-90) cc_final: 0.6898 (m-90) REVERT: H 232 MET cc_start: 0.7911 (tpp) cc_final: 0.7685 (tpp) REVERT: H 285 ILE cc_start: 0.8439 (pt) cc_final: 0.8232 (pp) REVERT: L 101 MET cc_start: 0.8108 (mtp) cc_final: 0.7416 (tpt) REVERT: L 236 GLN cc_start: 0.8484 (pm20) cc_final: 0.8207 (pm20) REVERT: L 407 MET cc_start: 0.8120 (mmm) cc_final: 0.7868 (mmm) REVERT: L 490 MET cc_start: 0.6004 (tpt) cc_final: 0.5701 (tpt) REVERT: L 533 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (p) REVERT: L 568 MET cc_start: 0.7292 (tpp) cc_final: 0.6560 (tmm) REVERT: M 291 MET cc_start: 0.8578 (mtm) cc_final: 0.8148 (mtm) REVERT: M 381 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: M 398 MET cc_start: 0.7850 (tpp) cc_final: 0.7488 (tpp) REVERT: M 408 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: N 36 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7427 (tm) REVERT: N 64 THR cc_start: 0.7425 (m) cc_final: 0.7159 (m) REVERT: N 74 MET cc_start: 0.7567 (mtm) cc_final: 0.7236 (mtp) REVERT: N 395 LYS cc_start: 0.8651 (tppp) cc_final: 0.8414 (tptm) REVERT: K 75 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8054 (tp) REVERT: K 86 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8047 (mmt180) REVERT: K 88 GLN cc_start: 0.8390 (mp10) cc_final: 0.8179 (mp10) REVERT: J 69 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7894 (t80) REVERT: J 88 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6878 (mm) outliers start: 114 outliers final: 67 residues processed: 467 average time/residue: 0.7292 time to fit residues: 407.3574 Evaluate side-chains 474 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 384 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 433 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 377 optimal weight: 9.9990 chunk 269 optimal weight: 20.0000 chunk 441 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN C 409 GLN B 196 ASN M 198 ASN K 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069128 restraints weight = 59722.340| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.38 r_work: 0.2852 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 37643 Z= 0.422 Angle : 2.532 50.651 51123 Z= 1.455 Chirality : 0.450 6.542 5708 Planarity : 0.005 0.071 6380 Dihedral : 8.058 126.546 5491 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 2.83 % Allowed : 18.07 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4601 helix: 1.47 (0.10), residues: 2681 sheet: -0.62 (0.30), residues: 303 loop : -0.41 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 26 TYR 0.020 0.002 TYR N 424 PHE 0.027 0.002 PHE L 341 TRP 0.029 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01195 (37607) covalent geometry : angle 2.21514 (51030) hydrogen bonds : bond 0.04993 ( 2127) hydrogen bonds : angle 4.70753 ( 6180) metal coordination : bond 0.04894 ( 36) metal coordination : angle 28.83919 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 388 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 158 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (mmtp) REVERT: F 182 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: F 255 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8171 (mmm160) REVERT: F 302 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 82 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: G 64 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8225 (ttp-170) REVERT: G 252 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: G 416 GLN cc_start: 0.8340 (tt0) cc_final: 0.8075 (mt0) REVERT: G 528 ASP cc_start: 0.8378 (t0) cc_final: 0.8093 (t0) REVERT: G 806 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: G 834 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.7942 (mp-120) REVERT: C 127 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: C 200 LYS cc_start: 0.8732 (tppt) cc_final: 0.8417 (tppp) REVERT: C 228 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6590 (p90) REVERT: C 576 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 39 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: B 91 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7646 (mmp80) REVERT: B 194 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6725 (mpp80) REVERT: B 219 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: I 153 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: H 60 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7492 (tm) REVERT: H 107 TRP cc_start: 0.7350 (m-90) cc_final: 0.7018 (m-90) REVERT: H 114 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7577 (pt) REVERT: H 232 MET cc_start: 0.7887 (tpp) cc_final: 0.7685 (tpp) REVERT: H 285 ILE cc_start: 0.8447 (pt) cc_final: 0.8240 (pp) REVERT: L 101 MET cc_start: 0.8188 (mtp) cc_final: 0.7413 (tpt) REVERT: L 568 MET cc_start: 0.7395 (tpp) cc_final: 0.6657 (tmm) REVERT: M 291 MET cc_start: 0.8576 (mtm) cc_final: 0.8142 (mtm) REVERT: M 381 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: M 398 MET cc_start: 0.7849 (tpp) cc_final: 0.7497 (tpp) REVERT: M 408 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: N 36 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7393 (tm) REVERT: N 64 THR cc_start: 0.7092 (m) cc_final: 0.6877 (m) REVERT: N 74 MET cc_start: 0.7520 (mtm) cc_final: 0.7163 (mtp) REVERT: K 25 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8155 (mmm160) REVERT: K 75 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8066 (tp) REVERT: K 88 GLN cc_start: 0.8427 (mp10) cc_final: 0.8162 (mm-40) REVERT: J 69 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7865 (t80) REVERT: J 88 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6862 (mm) outliers start: 107 outliers final: 67 residues processed: 457 average time/residue: 0.7154 time to fit residues: 389.5595 Evaluate side-chains 471 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 381 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 435 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 350 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 167 optimal weight: 40.0000 chunk 311 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 345 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN B 196 ASN M 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070256 restraints weight = 59479.500| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.39 r_work: 0.2876 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37643 Z= 0.402 Angle : 2.528 50.600 51123 Z= 1.452 Chirality : 0.448 6.489 5708 Planarity : 0.004 0.071 6380 Dihedral : 7.963 126.498 5491 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 2.43 % Allowed : 18.44 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4601 helix: 1.58 (0.10), residues: 2678 sheet: -0.68 (0.30), residues: 303 loop : -0.38 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 664 TYR 0.025 0.002 TYR J 109 PHE 0.026 0.001 PHE L 341 TRP 0.032 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01160 (37607) covalent geometry : angle 2.20890 (51030) hydrogen bonds : bond 0.04672 ( 2127) hydrogen bonds : angle 4.63537 ( 6180) metal coordination : bond 0.04057 ( 36) metal coordination : angle 28.88588 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 390 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 158 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8832 (mmtp) REVERT: F 182 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: F 255 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7652 (mtm180) REVERT: F 302 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 82 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: G 64 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.8194 (ttp-170) REVERT: G 252 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: G 416 GLN cc_start: 0.8310 (tt0) cc_final: 0.8065 (mt0) REVERT: G 528 ASP cc_start: 0.8351 (t0) cc_final: 0.8070 (t0) REVERT: G 664 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8346 (mtp-110) REVERT: G 806 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7972 (tp40) REVERT: G 834 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7904 (mp-120) REVERT: C 127 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: C 200 LYS cc_start: 0.8725 (tppt) cc_final: 0.8407 (tppp) REVERT: C 228 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6603 (p90) REVERT: C 576 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 39 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7380 (pmm) REVERT: B 91 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7685 (mmp80) REVERT: B 180 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7520 (ptm160) REVERT: B 194 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6693 (mpp80) REVERT: B 219 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: I 153 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: H 60 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7489 (tm) REVERT: H 107 TRP cc_start: 0.7332 (m-90) cc_final: 0.6994 (m-90) REVERT: H 114 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7505 (pt) REVERT: H 232 MET cc_start: 0.7844 (tpp) cc_final: 0.7626 (tpp) REVERT: L 101 MET cc_start: 0.8166 (mtp) cc_final: 0.7397 (tpt) REVERT: L 533 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8399 (p) REVERT: L 568 MET cc_start: 0.7270 (tpp) cc_final: 0.6566 (tmm) REVERT: M 291 MET cc_start: 0.8576 (mtm) cc_final: 0.8159 (mtm) REVERT: M 381 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: M 398 MET cc_start: 0.7854 (tpp) cc_final: 0.7443 (tpp) REVERT: M 408 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: N 36 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7457 (tm) REVERT: N 64 THR cc_start: 0.6859 (m) cc_final: 0.6587 (m) REVERT: N 74 MET cc_start: 0.7514 (mtm) cc_final: 0.7187 (mtp) REVERT: K 25 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8286 (mmt90) REVERT: K 75 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8041 (tp) REVERT: K 88 GLN cc_start: 0.8408 (mp10) cc_final: 0.8100 (mm-40) REVERT: J 69 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7911 (t80) REVERT: J 88 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6951 (mm) REVERT: J 160 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.8192 (ttp-170) outliers start: 92 outliers final: 59 residues processed: 455 average time/residue: 0.7147 time to fit residues: 390.4826 Evaluate side-chains 463 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 380 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 259 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 372 optimal weight: 0.0770 chunk 201 optimal weight: 0.6980 chunk 428 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 417 optimal weight: 9.9990 chunk 203 optimal weight: 0.1980 chunk 326 optimal weight: 8.9990 chunk 344 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN B 196 ASN M 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.095718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070651 restraints weight = 59145.675| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.37 r_work: 0.2886 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37643 Z= 0.397 Angle : 2.526 50.585 51123 Z= 1.452 Chirality : 0.447 6.469 5708 Planarity : 0.004 0.071 6380 Dihedral : 7.862 126.478 5491 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.51 % Allowed : 18.57 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 4601 helix: 1.61 (0.10), residues: 2681 sheet: -0.66 (0.30), residues: 290 loop : -0.35 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 664 TYR 0.022 0.002 TYR B 165 PHE 0.026 0.001 PHE L 341 TRP 0.037 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01152 (37607) covalent geometry : angle 2.20679 (51030) hydrogen bonds : bond 0.04533 ( 2127) hydrogen bonds : angle 4.59713 ( 6180) metal coordination : bond 0.03784 ( 36) metal coordination : angle 28.90713 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14799.88 seconds wall clock time: 251 minutes 51.67 seconds (15111.67 seconds total)