Starting phenix.real_space_refine on Mon Jul 6 16:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.map" model { file = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7m_13240/07_2026/7p7m_13240.cif" } resolution = 3.2 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= 0.015 sd= 0.054 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 12 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6171 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37390 Number of models: 1 Model: "" Number of chains: 25 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "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: 4728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4728 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2444 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4549 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 577} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 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: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1218 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HQH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'3PE': 5, 'LFA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 68.304 59.413 189.201 1.00 29.41 S ATOM 2741 SG CYS F 357 72.018 58.525 193.406 1.00 66.62 S ATOM 3062 SG CYS F 398 65.858 55.799 194.107 1.00 84.13 S ATOM 2697 SG CYS F 351 69.711 52.852 190.349 1.00 62.48 S ATOM 4054 SG CYS E 92 79.392 48.996 209.249 1.00 90.80 S ATOM 4088 SG CYS E 97 79.863 49.754 212.667 1.00 81.17 S ATOM 4366 SG CYS E 133 74.149 48.842 209.239 1.00110.33 S ATOM 4392 SG CYS E 137 73.610 49.597 212.541 1.00117.34 S ATOM 5476 SG CYS G 114 78.366 64.998 171.392 1.00 22.23 S ATOM 5416 SG CYS G 105 84.028 67.967 172.844 1.00 38.50 S ATOM 5436 SG CYS G 108 83.943 62.063 170.096 1.00 26.07 S ATOM 5830 SG CYS G 156 71.881 57.611 176.372 1.00 25.53 S ATOM 5811 SG CYS G 153 77.742 55.933 179.006 1.00 38.78 S ATOM 5859 SG CYS G 159 74.316 51.637 175.561 1.00 26.36 S ATOM 6203 SG CYS G 203 76.772 56.692 172.459 1.00 33.79 S ATOM 6428 SG CYS G 230 71.426 49.270 151.292 1.00 48.42 S ATOM 6713 SG CYS G 265 71.310 45.359 156.522 1.00 32.16 S ATOM 6476 SG CYS G 237 66.267 49.363 154.746 1.00 29.99 S ATOM 6452 SG CYS G 233 67.695 43.931 151.365 1.00 60.94 S ATOM 4877 SG CYS G 36 65.724 59.106 179.248 1.00 32.61 S ATOM 4953 SG CYS G 47 67.751 62.179 179.699 1.00 41.12 S ATOM 4979 SG CYS G 50 62.122 64.480 180.096 1.00 40.68 S ATOM 5128 SG CYS G 69 61.334 60.863 179.628 1.00 35.12 S ATOM 17223 SG CYS B 129 90.398 91.720 147.173 1.00 35.97 S ATOM 16720 SG CYS B 64 96.078 94.754 148.831 1.00 50.87 S ATOM 16714 SG CYS B 63 90.921 97.242 151.186 1.00 54.56 S ATOM 17440 SG CYS B 158 92.401 91.175 153.006 1.00 43.38 S ATOM 18818 SG CYS I 109 95.242 74.535 166.721 1.00 39.57 S ATOM 18481 SG CYS I 66 92.882 74.217 160.709 1.00 49.62 S ATOM 18441 SG CYS I 60 96.471 69.340 162.803 1.00 35.38 S ATOM 18459 SG CYS I 63 90.468 70.563 165.525 1.00 31.58 S ATOM 18771 SG CYS I 102 90.750 85.322 159.269 1.00 45.45 S ATOM 18746 SG CYS I 99 95.778 83.637 155.153 1.00 56.07 S ATOM 18789 SG CYS I 105 94.528 80.312 160.571 1.00 56.71 S ATOM 18504 SG CYS I 70 90.254 80.165 155.590 1.00 32.30 S Time building chain proxies: 6.05, per 1000 atoms: 0.16 Number of scatterers: 37390 At special positions: 0 Unit cell: (156.09, 220.22, 242, 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 267 16.00 P 12 15.00 O 6572 8.00 N 6171 7.00 C 24335 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: 3.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="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="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 102 " Number of angles added : 93 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8624 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.990A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.273A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.384A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE G 770 " --> pdb=" O ALA G 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 770' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.149A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.616A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.191A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.595A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 removed outlier: 3.936A pdb=" N PHE I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.464A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.253A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.106A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.578A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 removed outlier: 4.033A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.382A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.735A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.004A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.582A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 removed outlier: 4.043A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.300A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.428A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.426A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.076A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.814A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1703 hydrogen bonds defined for protein. 5109 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: 5.83 Time building geometry restraints manager: 3.88 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: 15914 1.42 - 1.64: 21903 1.64 - 1.86: 409 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38318 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" O13 3PE J 201 " pdb=" P 3PE J 201 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" O13 3PE A 201 " pdb=" P 3PE A 201 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" O13 3PE M 701 " pdb=" P 3PE M 701 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.61e+00 ... (remaining 38313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 51263 2.65 - 5.30: 581 5.30 - 7.95: 103 7.95 - 10.59: 28 10.59 - 13.24: 8 Bond angle restraints: 51983 Sorted by residual: angle pdb=" CA PRO G 872 " pdb=" N PRO G 872 " pdb=" CD PRO G 872 " ideal model delta sigma weight residual 112.00 101.39 10.61 1.40e+00 5.10e-01 5.74e+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 97.64 12.17 2.21e+00 2.05e-01 3.03e+01 angle pdb=" CA PRO C 35 " pdb=" N PRO C 35 " pdb=" CD PRO C 35 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.47e+01 angle pdb=" CB LYS E 116 " pdb=" CG LYS E 116 " pdb=" CD LYS E 116 " ideal model delta sigma weight residual 111.30 122.68 -11.38 2.30e+00 1.89e-01 2.45e+01 angle pdb=" CA VAL K 95 " pdb=" CB VAL K 95 " pdb=" CG1 VAL K 95 " ideal model delta sigma weight residual 110.40 118.53 -8.13 1.70e+00 3.46e-01 2.29e+01 ... (remaining 51978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 21892 33.91 - 67.83: 535 67.83 - 101.74: 31 101.74 - 135.65: 0 135.65 - 169.57: 1 Dihedral angle restraints: 22459 sinusoidal: 8976 harmonic: 13483 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 180.00 131.51 48.49 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.02 169.57 1 2.00e+01 2.50e-03 4.76e+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 180.00 146.34 33.66 0 5.00e+00 4.00e-02 4.53e+01 ... (remaining 22456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 5774 4.245 - 8.491: 0 8.491 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.226: 28 Chirality restraints: 5802 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.67 21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5799 not shown) Planarity restraints: 6502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 792 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CD GLU G 792 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU G 792 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU G 792 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO N 65 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 871 " -0.053 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO G 872 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 872 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 872 " -0.041 5.00e-02 4.00e+02 ... (remaining 6499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3885 2.75 - 3.29: 36642 3.29 - 3.83: 67715 3.83 - 4.36: 80840 4.36 - 4.90: 137653 Nonbonded interactions: 326735 Sorted by model distance: nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR H 128 " pdb=" O ALA J 60 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.242 3.040 nonbonded pdb=" O THR M 422 " pdb=" OG1 THR M 426 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR L 594 " pdb=" OD2 ASP N 229 " model vdw 2.273 3.040 ... (remaining 326730 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: 0.270 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 30.270 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.005 0.123 38354 Z= 0.204 Angle : 0.770 13.243 52076 Z= 0.383 Chirality : 1.468 21.226 5802 Planarity : 0.006 0.077 6502 Dihedral : 14.424 169.568 13835 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 0.39 % Allowed : 12.42 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.11), residues: 4680 helix: 0.34 (0.09), residues: 2665 sheet: -1.09 (0.26), residues: 333 loop : -1.24 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 288 TYR 0.032 0.002 TYR M 435 PHE 0.039 0.002 PHE L 341 TRP 0.027 0.001 TRP L 143 HIS 0.015 0.001 HIS G 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (38318) covalent geometry : angle 0.75287 / 0.38 (51983) hydrogen bonds : bond 0.05147 / 3.50 ( 1703) hydrogen bonds : angle 4.54325 / 3.20 ( 5109) metal coordination : bond 0.05456 / 3.49 ( 36) metal coordination : angle 3.87329 / 2.94 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 375 time to evaluate : 1.492 Fit side-chains REVERT: E 114 ASN cc_start: 0.8703 (m-40) cc_final: 0.8469 (p0) REVERT: E 116 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8691 (mmmt) REVERT: G 62 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7406 (mtp85) REVERT: G 312 LYS cc_start: 0.8491 (pttp) cc_final: 0.8051 (tptp) REVERT: H 238 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6219 (t80) REVERT: A 124 ASP cc_start: 0.8428 (m-30) cc_final: 0.7680 (p0) REVERT: M 325 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7675 (t80) REVERT: M 370 ASP cc_start: 0.8615 (t0) cc_final: 0.8314 (t70) REVERT: M 466 PHE cc_start: 0.8436 (m-10) cc_final: 0.7461 (t80) REVERT: N 485 MET cc_start: 0.3656 (mmt) cc_final: 0.3309 (mmt) REVERT: K 72 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8952 (mm-30) REVERT: J 3 PHE cc_start: 0.7989 (t80) cc_final: 0.7789 (t80) outliers start: 15 outliers final: 7 residues processed: 382 average time/residue: 0.2324 time to fit residues: 149.7368 Evaluate side-chains 358 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain N residue 321 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 110 HIS F 237 GLN E 98 HIS G 655 HIS G 768 ASN C 16 GLN C 359 HIS L 28 ASN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057826 restraints weight = 88914.024| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.72 r_work: 0.2843 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.267 38354 Z= 0.432 Angle : 2.510 51.188 52076 Z= 1.438 Chirality : 0.446 6.653 5802 Planarity : 0.005 0.069 6502 Dihedral : 7.709 171.253 5517 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 12.03 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.19 (0.12), residues: 4680 helix: 1.02 (0.10), residues: 2695 sheet: -1.04 (0.28), residues: 322 loop : -1.04 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 750 TYR 0.021 0.002 TYR N 424 PHE 0.025 0.002 PHE I 101 TRP 0.024 0.001 TRP L 143 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.43 (38318) covalent geometry : angle 2.18678 / 1.44 (51983) hydrogen bonds : bond 0.05354 / 3.65 ( 1703) hydrogen bonds : angle 4.25172 / 3.00 ( 5109) metal coordination : bond 0.04140 / 2.87 ( 36) metal coordination : angle 29.23181 / 20.66 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 1.431 Fit side-chains REVERT: F 94 MET cc_start: 0.8234 (mmm) cc_final: 0.7918 (mmm) REVERT: F 327 MET cc_start: 0.8714 (ttm) cc_final: 0.8429 (ttm) REVERT: E 46 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8445 (mm110) REVERT: E 86 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: G 178 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8683 (p90) REVERT: G 312 LYS cc_start: 0.8195 (pttp) cc_final: 0.7704 (tptp) REVERT: G 546 MET cc_start: 0.7742 (ttp) cc_final: 0.7455 (ttp) REVERT: G 792 GLU cc_start: 0.8005 (pp20) cc_final: 0.7796 (pp20) REVERT: G 793 ASN cc_start: 0.8272 (m-40) cc_final: 0.7795 (m-40) REVERT: B 193 TYR cc_start: 0.7707 (m-80) cc_final: 0.7000 (m-80) REVERT: A 30 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (ptt) REVERT: A 124 ASP cc_start: 0.8165 (m-30) cc_final: 0.7910 (p0) REVERT: M 466 PHE cc_start: 0.8120 (m-10) cc_final: 0.7405 (t80) REVERT: N 430 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8881 (p) REVERT: J 73 MET cc_start: 0.8822 (mtp) cc_final: 0.8437 (ttt) outliers start: 69 outliers final: 36 residues processed: 403 average time/residue: 0.2355 time to fit residues: 158.1417 Evaluate side-chains 370 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 178 HIS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 763 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 129 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 428 optimal weight: 30.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN E 46 GLN G 299 GLN H 138 ASN M 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058377 restraints weight = 88182.868| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.76 r_work: 0.2855 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38354 Z= 0.397 Angle : 2.497 50.951 52076 Z= 1.434 Chirality : 0.442 6.492 5802 Planarity : 0.004 0.062 6502 Dihedral : 7.422 172.384 5504 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.95 % Allowed : 12.42 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.62 (0.12), residues: 4680 helix: 1.38 (0.10), residues: 2685 sheet: -0.92 (0.28), residues: 319 loop : -0.87 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 664 TYR 0.024 0.001 TYR M 435 PHE 0.026 0.001 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.40 (38318) covalent geometry : angle 2.17318 / 1.43 (51983) hydrogen bonds : bond 0.04832 / 3.29 ( 1703) hydrogen bonds : angle 4.10177 / 2.89 ( 5109) metal coordination : bond 0.03699 / 2.46 ( 36) metal coordination : angle 29.18233 / 20.57 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 1.561 Fit side-chains REVERT: F 94 MET cc_start: 0.8226 (mmm) cc_final: 0.7995 (mmm) REVERT: F 327 MET cc_start: 0.8612 (ttm) cc_final: 0.8317 (ttm) REVERT: E 46 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (mm110) REVERT: E 86 ARG cc_start: 0.8878 (mtm-85) cc_final: 0.8143 (mtm-85) REVERT: G 312 LYS cc_start: 0.8190 (pttp) cc_final: 0.7684 (tptp) REVERT: G 546 MET cc_start: 0.7747 (ttp) cc_final: 0.7397 (ttp) REVERT: G 792 GLU cc_start: 0.8022 (pp20) cc_final: 0.7750 (pp20) REVERT: G 793 ASN cc_start: 0.8253 (m-40) cc_final: 0.7451 (m-40) REVERT: B 193 TYR cc_start: 0.7965 (m-80) cc_final: 0.7711 (m-80) REVERT: A 124 ASP cc_start: 0.8170 (m-30) cc_final: 0.7889 (p0) REVERT: M 325 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7918 (t80) REVERT: M 466 PHE cc_start: 0.8201 (m-10) cc_final: 0.7500 (t80) REVERT: N 430 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8839 (p) REVERT: N 485 MET cc_start: 0.4898 (mmt) cc_final: 0.4008 (mmt) REVERT: K 72 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8312 (mm-30) REVERT: J 72 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8935 (mtm) REVERT: J 73 MET cc_start: 0.8840 (mtp) cc_final: 0.8474 (ttt) outliers start: 75 outliers final: 46 residues processed: 408 average time/residue: 0.2249 time to fit residues: 152.5671 Evaluate side-chains 390 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 76 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 352 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 278 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.074557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057981 restraints weight = 87824.481| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.76 r_work: 0.2845 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38354 Z= 0.401 Angle : 2.500 50.967 52076 Z= 1.435 Chirality : 0.442 6.499 5802 Planarity : 0.004 0.064 6502 Dihedral : 7.314 172.270 5502 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 2.16 % Allowed : 12.52 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.75 (0.12), residues: 4680 helix: 1.49 (0.10), residues: 2693 sheet: -0.99 (0.28), residues: 332 loop : -0.80 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 288 TYR 0.022 0.001 TYR M 435 PHE 0.025 0.001 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01153 / 0.40 (38318) covalent geometry : angle 2.17530 / 1.43 (51983) hydrogen bonds : bond 0.04926 / 3.36 ( 1703) hydrogen bonds : angle 4.09769 / 2.89 ( 5109) metal coordination : bond 0.03314 / 2.18 ( 36) metal coordination : angle 29.22937 / 20.62 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 354 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: F 94 MET cc_start: 0.8373 (mmm) cc_final: 0.8009 (mmm) REVERT: F 327 MET cc_start: 0.8625 (ttm) cc_final: 0.8345 (ttm) REVERT: G 295 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (mt) REVERT: G 312 LYS cc_start: 0.8057 (pttp) cc_final: 0.7608 (tptp) REVERT: G 546 MET cc_start: 0.7821 (ttp) cc_final: 0.7455 (ttp) REVERT: G 792 GLU cc_start: 0.8071 (pp20) cc_final: 0.7788 (pp20) REVERT: G 793 ASN cc_start: 0.8274 (m-40) cc_final: 0.7231 (m-40) REVERT: G 906 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7720 (mmtm) REVERT: B 193 TYR cc_start: 0.7840 (m-80) cc_final: 0.7595 (m-80) REVERT: H 242 TYR cc_start: 0.8942 (m-80) cc_final: 0.8529 (m-80) REVERT: A 124 ASP cc_start: 0.8135 (m-30) cc_final: 0.7843 (p0) REVERT: L 328 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7010 (m100) REVERT: L 407 MET cc_start: 0.8338 (mtt) cc_final: 0.8130 (mtt) REVERT: M 466 PHE cc_start: 0.8208 (m-10) cc_final: 0.7508 (t80) REVERT: N 183 ASP cc_start: 0.8970 (t0) cc_final: 0.8750 (t0) REVERT: N 379 MET cc_start: 0.9017 (mmt) cc_final: 0.8762 (mmt) REVERT: N 430 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8855 (p) REVERT: K 72 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8352 (mm-30) REVERT: J 72 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: J 73 MET cc_start: 0.8882 (mtp) cc_final: 0.8516 (ttt) outliers start: 83 outliers final: 60 residues processed: 410 average time/residue: 0.2299 time to fit residues: 157.3169 Evaluate side-chains 405 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 157 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 278 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 222 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 427 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.075667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059191 restraints weight = 87596.486| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.76 r_work: 0.2876 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38354 Z= 0.385 Angle : 2.493 50.737 52076 Z= 1.432 Chirality : 0.441 6.471 5802 Planarity : 0.004 0.065 6502 Dihedral : 7.123 172.001 5502 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.16 % Allowed : 13.01 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.96 (0.13), residues: 4680 helix: 1.66 (0.10), residues: 2690 sheet: -0.86 (0.28), residues: 328 loop : -0.70 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 804 TYR 0.025 0.001 TYR M 435 PHE 0.025 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.38 (38318) covalent geometry : angle 2.16721 / 1.43 (51983) hydrogen bonds : bond 0.04513 / 3.08 ( 1703) hydrogen bonds : angle 3.97606 / 2.81 ( 5109) metal coordination : bond 0.02707 / 1.76 ( 36) metal coordination : angle 29.25440 / 20.73 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 366 time to evaluate : 1.427 Fit side-chains REVERT: F 94 MET cc_start: 0.8375 (mmm) cc_final: 0.8055 (mmm) REVERT: F 237 GLN cc_start: 0.9005 (mt0) cc_final: 0.8468 (mp10) REVERT: E 46 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8372 (mm-40) REVERT: E 165 TYR cc_start: 0.7719 (m-80) cc_final: 0.7423 (m-80) REVERT: G 312 LYS cc_start: 0.8034 (pttp) cc_final: 0.7634 (tptp) REVERT: G 546 MET cc_start: 0.7725 (ttp) cc_final: 0.7299 (ttp) REVERT: G 792 GLU cc_start: 0.8065 (pp20) cc_final: 0.7757 (pp20) REVERT: G 793 ASN cc_start: 0.8273 (m-40) cc_final: 0.7107 (m-40) REVERT: G 906 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7630 (mmtm) REVERT: B 193 TYR cc_start: 0.7626 (m-80) cc_final: 0.7424 (m-80) REVERT: I 153 MET cc_start: 0.7894 (mmt) cc_final: 0.7643 (mmt) REVERT: H 36 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: A 124 ASP cc_start: 0.8128 (m-30) cc_final: 0.7793 (p0) REVERT: L 328 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.6742 (m100) REVERT: M 325 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7927 (t80) REVERT: M 466 PHE cc_start: 0.8191 (m-10) cc_final: 0.7491 (t80) REVERT: N 379 MET cc_start: 0.9036 (mmt) cc_final: 0.8823 (mmt) REVERT: N 430 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (p) REVERT: K 72 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8327 (mm-30) REVERT: J 68 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9027 (t) REVERT: J 72 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8902 (mtm) REVERT: J 73 MET cc_start: 0.8929 (mtp) cc_final: 0.8562 (ttt) outliers start: 83 outliers final: 56 residues processed: 426 average time/residue: 0.2113 time to fit residues: 150.6140 Evaluate side-chains 412 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 350 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 405 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 416 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 170 GLN M 308 GLN J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057203 restraints weight = 87661.866| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.70 r_work: 0.2828 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38354 Z= 0.420 Angle : 2.510 50.867 52076 Z= 1.438 Chirality : 0.443 6.527 5802 Planarity : 0.004 0.063 6502 Dihedral : 7.349 172.984 5502 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 13.12 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 0.88 (0.13), residues: 4680 helix: 1.58 (0.10), residues: 2695 sheet: -1.01 (0.28), residues: 344 loop : -0.70 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.019 0.002 TYR N 424 PHE 0.023 0.002 PHE L 341 TRP 0.025 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01185 / 0.42 (38318) covalent geometry : angle 2.18458 / 1.44 (51983) hydrogen bonds : bond 0.05240 / 3.58 ( 1703) hydrogen bonds : angle 4.16456 / 2.94 ( 5109) metal coordination : bond 0.03560 / 2.50 ( 36) metal coordination : angle 29.32375 / 20.69 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 347 time to evaluate : 1.364 Fit side-chains REVERT: F 94 MET cc_start: 0.8554 (mmm) cc_final: 0.8111 (mmm) REVERT: E 46 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8494 (mm-40) REVERT: G 312 LYS cc_start: 0.8064 (pttp) cc_final: 0.7679 (tptp) REVERT: G 593 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7262 (ttt) REVERT: G 670 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: G 792 GLU cc_start: 0.8126 (pp20) cc_final: 0.7822 (pp20) REVERT: G 793 ASN cc_start: 0.8271 (m-40) cc_final: 0.7111 (m-40) REVERT: B 193 TYR cc_start: 0.7691 (m-80) cc_final: 0.7400 (m-80) REVERT: I 153 MET cc_start: 0.7893 (mmt) cc_final: 0.7619 (mmt) REVERT: H 36 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: H 242 TYR cc_start: 0.9012 (m-80) cc_final: 0.8779 (m-80) REVERT: A 124 ASP cc_start: 0.8130 (m-30) cc_final: 0.7889 (p0) REVERT: L 328 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7180 (m100) REVERT: L 407 MET cc_start: 0.8160 (mtt) cc_final: 0.7944 (mtt) REVERT: M 466 PHE cc_start: 0.8237 (m-10) cc_final: 0.7495 (t80) REVERT: N 379 MET cc_start: 0.9101 (mmt) cc_final: 0.8879 (mmt) REVERT: N 430 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8934 (p) REVERT: J 68 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9076 (t) REVERT: J 72 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8891 (mtm) REVERT: J 73 MET cc_start: 0.8943 (mtp) cc_final: 0.8608 (ttt) outliers start: 93 outliers final: 68 residues processed: 414 average time/residue: 0.2132 time to fit residues: 147.3416 Evaluate side-chains 414 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 271 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 416 optimal weight: 9.9990 chunk 371 optimal weight: 0.9980 chunk 331 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 388 optimal weight: 0.0980 chunk 147 optimal weight: 7.9990 chunk 379 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.075511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059095 restraints weight = 87789.330| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.76 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 38354 Z= 0.384 Angle : 2.497 50.823 52076 Z= 1.433 Chirality : 0.441 6.460 5802 Planarity : 0.004 0.065 6502 Dihedral : 7.154 172.764 5502 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.16 % Allowed : 13.64 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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 (0.13), residues: 4680 helix: 1.74 (0.10), residues: 2693 sheet: -0.82 (0.29), residues: 327 loop : -0.63 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 664 TYR 0.025 0.001 TYR M 435 PHE 0.025 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.38 (38318) covalent geometry : angle 2.17004 / 1.43 (51983) hydrogen bonds : bond 0.04562 / 3.11 ( 1703) hydrogen bonds : angle 3.98824 / 2.82 ( 5109) metal coordination : bond 0.02699 / 1.85 ( 36) metal coordination : angle 29.31132 / 20.82 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 1.343 Fit side-chains REVERT: F 94 MET cc_start: 0.8591 (mmm) cc_final: 0.8259 (mmm) REVERT: F 237 GLN cc_start: 0.9021 (mt0) cc_final: 0.8499 (mp10) REVERT: E 46 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8532 (mm-40) REVERT: E 60 ASP cc_start: 0.8492 (p0) cc_final: 0.8068 (p0) REVERT: E 112 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8360 (ttmm) REVERT: E 165 TYR cc_start: 0.7747 (m-80) cc_final: 0.7432 (m-80) REVERT: G 312 LYS cc_start: 0.8054 (pttp) cc_final: 0.7694 (tptp) REVERT: G 670 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: G 792 GLU cc_start: 0.8079 (pp20) cc_final: 0.7754 (pp20) REVERT: G 793 ASN cc_start: 0.8230 (m-40) cc_final: 0.6989 (m-40) REVERT: I 153 MET cc_start: 0.7958 (mmt) cc_final: 0.7704 (mmt) REVERT: H 36 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8346 (tp30) REVERT: A 124 ASP cc_start: 0.8100 (m-30) cc_final: 0.7751 (p0) REVERT: L 328 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.6751 (m100) REVERT: M 325 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7881 (t80) REVERT: M 466 PHE cc_start: 0.8227 (m-10) cc_final: 0.7500 (t80) REVERT: N 379 MET cc_start: 0.9140 (mmt) cc_final: 0.8934 (mmt) REVERT: N 430 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8814 (p) REVERT: K 72 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8287 (mm-30) REVERT: J 68 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9013 (t) REVERT: J 72 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8866 (mtm) outliers start: 83 outliers final: 61 residues processed: 423 average time/residue: 0.2155 time to fit residues: 151.7246 Evaluate side-chains 418 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 864 TYR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 362 TRP Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 200 optimal weight: 2.9990 chunk 459 optimal weight: 6.9990 chunk 443 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 374 optimal weight: 7.9990 chunk 384 optimal weight: 5.9990 chunk 268 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059219 restraints weight = 87138.143| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.76 r_work: 0.2876 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.251 38354 Z= 0.386 Angle : 2.498 50.820 52076 Z= 1.433 Chirality : 0.440 6.451 5802 Planarity : 0.004 0.067 6502 Dihedral : 7.058 172.613 5502 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.08 % Allowed : 14.00 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.15 (0.13), residues: 4680 helix: 1.78 (0.10), residues: 2694 sheet: -0.77 (0.29), residues: 327 loop : -0.57 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 804 TYR 0.028 0.001 TYR B 193 PHE 0.025 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.39 (38318) covalent geometry : angle 2.17076 / 1.43 (51983) hydrogen bonds : bond 0.04503 / 3.07 ( 1703) hydrogen bonds : angle 3.95278 / 2.79 ( 5109) metal coordination : bond 0.02731 / 1.93 ( 36) metal coordination : angle 29.33987 / 20.82 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 362 time to evaluate : 1.441 Fit side-chains REVERT: F 94 MET cc_start: 0.8518 (mmm) cc_final: 0.8174 (mmm) REVERT: E 46 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8474 (mm-40) REVERT: E 60 ASP cc_start: 0.8492 (p0) cc_final: 0.8063 (p0) REVERT: E 112 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8374 (ttmm) REVERT: E 116 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8729 (mmmt) REVERT: E 165 TYR cc_start: 0.7722 (m-80) cc_final: 0.7413 (m-80) REVERT: G 312 LYS cc_start: 0.8054 (pttp) cc_final: 0.7698 (tptp) REVERT: G 670 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: G 792 GLU cc_start: 0.8070 (pp20) cc_final: 0.7743 (pp20) REVERT: G 793 ASN cc_start: 0.8196 (m-40) cc_final: 0.6915 (m-40) REVERT: B 193 TYR cc_start: 0.7751 (m-80) cc_final: 0.7536 (m-80) REVERT: I 153 MET cc_start: 0.8034 (mmt) cc_final: 0.7768 (mmt) REVERT: H 36 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: H 229 TYR cc_start: 0.9051 (m-80) cc_final: 0.8846 (m-80) REVERT: A 124 ASP cc_start: 0.8110 (m-30) cc_final: 0.7782 (p0) REVERT: L 328 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.6701 (m100) REVERT: M 466 PHE cc_start: 0.8199 (m-10) cc_final: 0.7498 (t80) REVERT: N 430 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8825 (p) REVERT: K 72 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8303 (mm-30) REVERT: J 68 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8969 (t) REVERT: J 72 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8841 (mtm) outliers start: 80 outliers final: 66 residues processed: 420 average time/residue: 0.2085 time to fit residues: 146.4805 Evaluate side-chains 423 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 351 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 362 TRP Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 119 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 400 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.075148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058688 restraints weight = 87932.379| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.76 r_work: 0.2861 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.249 38354 Z= 0.393 Angle : 2.503 50.795 52076 Z= 1.435 Chirality : 0.441 6.447 5802 Planarity : 0.004 0.068 6502 Dihedral : 7.096 172.899 5502 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.13 % Allowed : 14.10 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.11 (0.13), residues: 4680 helix: 1.74 (0.10), residues: 2692 sheet: -0.85 (0.28), residues: 333 loop : -0.56 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 804 TYR 0.022 0.001 TYR N 424 PHE 0.025 0.001 PHE N 72 TRP 0.022 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.39 (38318) covalent geometry : angle 2.17592 / 1.43 (51983) hydrogen bonds : bond 0.04672 / 3.20 ( 1703) hydrogen bonds : angle 4.00684 / 2.83 ( 5109) metal coordination : bond 0.02867 / 2.02 ( 36) metal coordination : angle 29.34458 / 20.81 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 358 time to evaluate : 1.409 Fit side-chains REVERT: F 94 MET cc_start: 0.8584 (mmm) cc_final: 0.8198 (mmm) REVERT: F 237 GLN cc_start: 0.9013 (mt0) cc_final: 0.8535 (mp10) REVERT: E 46 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8500 (mm-40) REVERT: E 60 ASP cc_start: 0.8525 (p0) cc_final: 0.8252 (p0) REVERT: E 165 TYR cc_start: 0.7708 (m-80) cc_final: 0.7388 (m-80) REVERT: G 312 LYS cc_start: 0.8077 (pttp) cc_final: 0.7707 (tptp) REVERT: G 670 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: G 792 GLU cc_start: 0.8087 (pp20) cc_final: 0.7778 (pp20) REVERT: G 793 ASN cc_start: 0.8209 (m-40) cc_final: 0.7024 (m-40) REVERT: I 153 MET cc_start: 0.8010 (mmt) cc_final: 0.7735 (mmt) REVERT: H 36 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: A 124 ASP cc_start: 0.8124 (m-30) cc_final: 0.7792 (p0) REVERT: L 243 MET cc_start: 0.8189 (mmm) cc_final: 0.7925 (mmm) REVERT: L 328 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.6830 (m100) REVERT: M 466 PHE cc_start: 0.8218 (m-10) cc_final: 0.7515 (t80) REVERT: N 379 MET cc_start: 0.9040 (mmt) cc_final: 0.8822 (mmm) REVERT: N 430 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8813 (p) REVERT: K 72 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8313 (mm-30) REVERT: J 68 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.8983 (t) REVERT: J 72 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8854 (mtm) outliers start: 82 outliers final: 69 residues processed: 417 average time/residue: 0.2108 time to fit residues: 146.4710 Evaluate side-chains 426 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 351 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 371 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 380 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 233 optimal weight: 0.0980 chunk 132 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 385 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.075439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059021 restraints weight = 87449.539| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.76 r_work: 0.2871 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.250 38354 Z= 0.388 Angle : 2.501 50.784 52076 Z= 1.434 Chirality : 0.441 6.443 5802 Planarity : 0.004 0.069 6502 Dihedral : 7.074 173.027 5502 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.05 % Allowed : 14.21 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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: 1.16 (0.13), residues: 4680 helix: 1.79 (0.10), residues: 2692 sheet: -0.85 (0.28), residues: 333 loop : -0.54 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 804 TYR 0.023 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.022 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01134 / 0.39 (38318) covalent geometry : angle 2.17332 / 1.43 (51983) hydrogen bonds : bond 0.04551 / 3.11 ( 1703) hydrogen bonds : angle 3.97681 / 2.81 ( 5109) metal coordination : bond 0.02743 / 1.93 ( 36) metal coordination : angle 29.34957 / 20.83 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 1.371 Fit side-chains REVERT: F 94 MET cc_start: 0.8558 (mmm) cc_final: 0.8188 (mmm) REVERT: E 46 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8496 (mm-40) REVERT: E 60 ASP cc_start: 0.8559 (p0) cc_final: 0.8274 (p0) REVERT: E 112 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8384 (ttmm) REVERT: E 165 TYR cc_start: 0.7708 (m-80) cc_final: 0.7399 (m-80) REVERT: G 312 LYS cc_start: 0.8076 (pttp) cc_final: 0.7716 (tptp) REVERT: G 670 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: G 792 GLU cc_start: 0.8122 (pp20) cc_final: 0.7807 (pp20) REVERT: G 793 ASN cc_start: 0.8179 (m-40) cc_final: 0.7064 (m-40) REVERT: B 193 TYR cc_start: 0.7811 (m-80) cc_final: 0.7523 (m-80) REVERT: I 153 MET cc_start: 0.8047 (mmt) cc_final: 0.7779 (mmt) REVERT: H 36 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8319 (tp30) REVERT: A 124 ASP cc_start: 0.8116 (m-30) cc_final: 0.7781 (p0) REVERT: L 243 MET cc_start: 0.8192 (mmm) cc_final: 0.7948 (mmm) REVERT: L 328 TRP cc_start: 0.8444 (OUTLIER) cc_final: 0.6704 (m100) REVERT: M 466 PHE cc_start: 0.8209 (m-10) cc_final: 0.7505 (t80) REVERT: N 104 GLU cc_start: 0.8613 (mp0) cc_final: 0.8246 (mp0) REVERT: N 183 ASP cc_start: 0.8780 (t0) cc_final: 0.8546 (t0) REVERT: N 430 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8799 (p) REVERT: K 72 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8309 (mm-30) REVERT: J 68 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.8962 (t) REVERT: J 72 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8835 (mtm) outliers start: 79 outliers final: 69 residues processed: 418 average time/residue: 0.2149 time to fit residues: 150.4330 Evaluate side-chains 429 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 362 TRP Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 86 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 382 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 chunk 135 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 364 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.074277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057934 restraints weight = 87452.159| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.69 r_work: 0.2846 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38354 Z= 0.406 Angle : 2.509 50.828 52076 Z= 1.438 Chirality : 0.442 6.460 5802 Planarity : 0.004 0.069 6502 Dihedral : 7.221 173.884 5502 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.08 % Allowed : 14.13 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % 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 (0.13), residues: 4680 helix: 1.70 (0.10), residues: 2697 sheet: -0.87 (0.28), residues: 328 loop : -0.59 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 804 TYR 0.020 0.002 TYR N 424 PHE 0.026 0.001 PHE N 72 TRP 0.023 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01161 / 0.41 (38318) covalent geometry : angle 2.18355 / 1.43 (51983) hydrogen bonds : bond 0.04995 / 3.41 ( 1703) hydrogen bonds : angle 4.10683 / 2.90 ( 5109) metal coordination : bond 0.03115 / 2.17 ( 36) metal coordination : angle 29.33605 / 20.77 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10540.35 seconds wall clock time: 180 minutes 45.08 seconds (10845.08 seconds total)