Starting phenix.real_space_refine on Mon Jul 6 17:30:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p63_13216/07_2026/7p63_13216.map" } resolution = 3.4 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= 0.002 sd= 0.009 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 11 5.49 5 S 267 5.16 5 C 24556 2.51 5 N 6265 2.21 5 O 6638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 37770 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: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7012 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4762 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1672 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 195} 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: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 4560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4560 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 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: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3614 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 77.428 60.861 190.533 1.00 38.66 S ATOM 2741 SG CYS F 357 81.028 60.754 195.126 1.00 32.68 S ATOM 3062 SG CYS F 398 75.234 57.498 195.785 1.00 49.01 S ATOM 2697 SG CYS F 351 79.655 54.746 192.305 1.00 14.69 S ATOM 4054 SG CYS E 92 88.332 53.081 211.981 1.00 40.80 S ATOM 4088 SG CYS E 97 88.392 54.133 215.354 1.00 51.52 S ATOM 4366 SG CYS E 133 83.036 52.387 211.654 1.00 48.16 S ATOM 4392 SG CYS E 137 82.235 53.337 214.766 1.00 36.95 S ATOM 5472 SG CYS G 114 88.001 66.538 173.122 1.00 26.39 S ATOM 5412 SG CYS G 105 93.248 70.238 174.726 1.00 16.65 S ATOM 5432 SG CYS G 108 93.993 64.332 172.243 1.00 16.90 S ATOM 5826 SG CYS G 156 82.131 58.743 178.191 1.00 30.27 S ATOM 5807 SG CYS G 153 88.021 57.966 181.170 1.00 34.08 S ATOM 5855 SG CYS G 159 85.334 53.065 177.907 1.00 27.41 S ATOM 6199 SG CYS G 203 87.292 58.178 174.581 1.00 0.00 S ATOM 6424 SG CYS G 230 84.031 49.265 153.699 1.00 18.83 S ATOM 6709 SG CYS G 265 84.039 45.690 159.249 1.00 10.53 S ATOM 6472 SG CYS G 237 78.676 48.838 156.794 1.00 6.87 S ATOM 6448 SG CYS G 233 81.077 43.449 154.001 1.00 7.38 S ATOM 4877 SG CYS G 36 75.768 59.907 180.661 1.00 22.33 S ATOM 4953 SG CYS G 47 77.301 63.368 181.025 1.00 40.49 S ATOM 4979 SG CYS G 50 71.515 64.856 181.191 1.00 41.74 S ATOM 5124 SG CYS G 69 71.035 61.296 180.735 1.00 24.92 S ATOM 17351 SG CYS B 129 98.011 93.016 148.307 1.00 35.33 S ATOM 16848 SG CYS B 64 103.168 96.969 149.639 1.00 22.01 S ATOM 16842 SG CYS B 63 97.648 98.958 151.686 1.00 43.29 S ATOM 17568 SG CYS B 158 100.083 93.363 154.107 1.00 43.27 S ATOM 18899 SG CYS I 102 98.668 87.668 160.368 1.00 24.52 S ATOM 18874 SG CYS I 99 104.041 86.285 156.584 1.00 25.84 S ATOM 18917 SG CYS I 105 102.933 83.127 162.048 1.00 32.02 S ATOM 18632 SG CYS I 70 98.825 82.315 156.980 1.00 6.84 S ATOM 18946 SG CYS I 109 103.855 77.746 168.490 1.00 34.59 S ATOM 18609 SG CYS I 66 101.786 76.837 162.391 1.00 17.88 S ATOM 18569 SG CYS I 60 105.825 72.572 164.905 1.00 42.18 S ATOM 18587 SG CYS I 63 99.593 73.196 167.326 1.00 11.44 S Time building chain proxies: 6.69, per 1000 atoms: 0.18 Number of scatterers: 37770 At special positions: 0 Unit cell: (161.12, 217.3, 242.74, 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 11 15.00 O 6638 8.00 N 6265 7.00 C 24556 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " 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="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 51.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 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: 4.756A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.772A 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: 4.422A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.809A 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: 5.390A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) removed outlier: 4.327A 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 removed outlier: 4.292A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for '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: 5.010A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.665A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 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 removed outlier: 4.181A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) 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 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: 4.541A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 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: 4.721A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.491A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.585A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.798A 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 68 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.321A 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 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: 4.974A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.865A 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: 4.696A 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: 4.872A 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: 4.539A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.226A 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 removed outlier: 4.049A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) 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 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: 4.423A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.108A 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 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: 4.242A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.505A 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: 3.987A 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 80 through 84 Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.314A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1704 hydrogen bonds defined for protein. 5112 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: 5.51 Time building geometry restraints manager: 3.94 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: 16102 1.42 - 1.64: 22113 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38716 Sorted by residual: bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.97e+00 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 8.82e+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 8.68e+00 bond pdb=" O13 3PE M1002 " pdb=" P 3PE M1002 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.51e+00 ... (remaining 38711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 51587 2.42 - 4.85: 774 4.85 - 7.27: 130 7.27 - 9.69: 35 9.69 - 12.12: 11 Bond angle restraints: 52537 Sorted by residual: angle pdb=" CA MET F 161 " pdb=" CB MET F 161 " pdb=" CG MET F 161 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+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 98.48 11.33 2.21e+00 2.05e-01 2.63e+01 angle pdb=" CA GLN N 180 " pdb=" CB GLN N 180 " pdb=" CG GLN N 180 " ideal model delta sigma weight residual 114.10 122.87 -8.77 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CB GLN N 180 " pdb=" CG GLN N 180 " pdb=" CD GLN N 180 " ideal model delta sigma weight residual 112.60 120.05 -7.45 1.70e+00 3.46e-01 1.92e+01 angle pdb=" CA ILE K 33 " pdb=" CB ILE K 33 " pdb=" CG1 ILE K 33 " ideal model delta sigma weight residual 110.40 117.79 -7.39 1.70e+00 3.46e-01 1.89e+01 ... (remaining 52532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 22009 33.87 - 67.73: 629 67.73 - 101.60: 34 101.60 - 135.47: 0 135.47 - 169.33: 1 Dihedral angle restraints: 22673 sinusoidal: 9040 harmonic: 13633 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 180.00 133.40 46.60 0 5.00e+00 4.00e-02 8.69e+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 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+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 88.26 169.33 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.243: 5831 4.243 - 8.486: 0 8.486 - 12.729: 0 12.729 - 16.972: 0 16.972 - 21.215: 28 Chirality restraints: 5859 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 -10.66 21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5856 not shown) Planarity restraints: 6577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 701 " 0.029 2.00e-02 2.50e+03 4.91e-02 7.22e+01 pdb=" C1M DCQ C 701 " 0.055 2.00e-02 2.50e+03 pdb=" C2 DCQ C 701 " 0.010 2.00e-02 2.50e+03 pdb=" C3 DCQ C 701 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DCQ C 701 " 0.027 2.00e-02 2.50e+03 pdb=" C5 DCQ C 701 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DCQ C 701 " -0.010 2.00e-02 2.50e+03 pdb=" C7 DCQ C 701 " -0.065 2.00e-02 2.50e+03 pdb=" O2 DCQ C 701 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ C 701 " -0.105 2.00e-02 2.50e+03 pdb=" O4 DCQ C 701 " 0.089 2.00e-02 2.50e+03 pdb=" O5 DCQ C 701 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 682 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO G 683 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO G 683 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 683 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO N 5 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.054 5.00e-02 4.00e+02 ... (remaining 6574 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1467 2.72 - 3.27: 37342 3.27 - 3.81: 66648 3.81 - 4.36: 83979 4.36 - 4.90: 141149 Nonbonded interactions: 330585 Sorted by model distance: nonbonded pdb=" O LEU M 16 " pdb=" OG1 THR M 20 " model vdw 2.178 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.230 3.040 nonbonded pdb=" O ILE M 315 " pdb=" OG1 THR M 318 " model vdw 2.242 3.040 nonbonded pdb=" O ARG F 39 " pdb=" OG1 THR F 43 " model vdw 2.250 3.040 ... (remaining 330580 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.590 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 0.089 38752 Z= 0.205 Angle : 0.781 15.696 52630 Z= 0.393 Chirality : 1.461 21.215 5859 Planarity : 0.006 0.121 6577 Dihedral : 15.284 169.335 13955 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 0.49 % Allowed : 16.15 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -0.69 (0.11), residues: 4738 helix: 0.24 (0.09), residues: 2678 sheet: -0.74 (0.28), residues: 321 loop : -1.40 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 63 TYR 0.037 0.002 TYR L 428 PHE 0.044 0.002 PHE M 175 TRP 0.016 0.001 TRP L 143 HIS 0.010 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (38716) covalent geometry : angle 0.76561 / 0.39 (52537) hydrogen bonds : bond 0.05110 / 3.35 ( 1704) hydrogen bonds : angle 4.69403 / 3.36 ( 5112) metal coordination : bond 0.05438 / 3.51 ( 36) metal coordination : angle 3.77518 / 2.77 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 545 time to evaluate : 1.382 Fit side-chains REVERT: F 48 ASP cc_start: 0.7424 (m-30) cc_final: 0.7201 (p0) REVERT: F 106 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7572 (tm-30) REVERT: G 583 ASN cc_start: 0.8510 (m-40) cc_final: 0.7667 (t0) REVERT: G 750 ARG cc_start: 0.8535 (ptt90) cc_final: 0.8335 (ptt-90) REVERT: C 206 MET cc_start: 0.7285 (mmm) cc_final: 0.6937 (mmm) REVERT: C 555 MET cc_start: 0.8691 (mtt) cc_final: 0.8237 (mtt) REVERT: C 581 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 170 MET cc_start: 0.8136 (mtp) cc_final: 0.7718 (mtm) REVERT: H 282 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: A 88 TRP cc_start: 0.8527 (t60) cc_final: 0.8327 (t60) REVERT: L 119 TYR cc_start: 0.8849 (m-10) cc_final: 0.8557 (m-80) REVERT: L 236 GLN cc_start: 0.8700 (pt0) cc_final: 0.8261 (pm20) REVERT: L 265 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8762 (mt) REVERT: L 400 ASP cc_start: 0.9118 (m-30) cc_final: 0.8398 (t0) REVERT: N 30 TRP cc_start: 0.7917 (t-100) cc_final: 0.7235 (t60) REVERT: N 482 MET cc_start: 0.6904 (tmm) cc_final: 0.6379 (ppp) REVERT: K 97 GLU cc_start: 0.7282 (tt0) cc_final: 0.6980 (tt0) REVERT: J 85 ARG cc_start: 0.5564 (tpt90) cc_final: 0.5183 (tpt-90) REVERT: J 91 GLN cc_start: 0.5977 (mp10) cc_final: 0.5089 (pm20) outliers start: 19 outliers final: 4 residues processed: 557 average time/residue: 0.2112 time to fit residues: 195.6000 Evaluate side-chains 509 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 502 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain K residue 89 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 470 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 291 GLN F 304 HIS ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 359 HIS B 43 ASN H 45 ASN M 64 GLN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 91 ASN J 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077787 restraints weight = 72378.252| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 0.87 r_work: 0.3029 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.269 38752 Z= 0.405 Angle : 2.490 51.257 52630 Z= 1.430 Chirality : 0.441 6.732 5859 Planarity : 0.005 0.082 6577 Dihedral : 6.768 169.384 5508 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.44 % Allowed : 14.79 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.11 (0.12), residues: 4738 helix: 0.98 (0.10), residues: 2674 sheet: -0.80 (0.29), residues: 321 loop : -1.12 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 416 TYR 0.024 0.002 TYR H 242 PHE 0.029 0.002 PHE L 341 TRP 0.018 0.001 TRP F 353 HIS 0.006 0.001 HIS C 123 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.40 (38716) covalent geometry : angle 2.17365 / 1.43 (52537) hydrogen bonds : bond 0.04856 / 3.19 ( 1704) hydrogen bonds : angle 4.19795 / 3.01 ( 5112) metal coordination : bond 0.04006 / 2.50 ( 36) metal coordination : angle 28.98801 / 19.92 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 519 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: F 161 MET cc_start: 0.6404 (tpt) cc_final: 0.6068 (tpt) REVERT: G 150 MET cc_start: 0.8876 (tpp) cc_final: 0.8631 (tpp) REVERT: G 583 ASN cc_start: 0.7833 (m-40) cc_final: 0.7538 (t0) REVERT: G 740 MET cc_start: 0.8567 (ptp) cc_final: 0.8352 (pmm) REVERT: G 901 HIS cc_start: 0.7340 (m-70) cc_final: 0.7118 (m-70) REVERT: C 127 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8338 (t80) REVERT: C 206 MET cc_start: 0.7314 (mmm) cc_final: 0.7062 (mmm) REVERT: B 94 ASP cc_start: 0.7236 (m-30) cc_final: 0.6426 (t0) REVERT: H 31 PHE cc_start: 0.6285 (m-10) cc_final: 0.6047 (m-10) REVERT: A 62 LEU cc_start: 0.5241 (mp) cc_final: 0.5024 (mp) REVERT: L 144 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7294 (mm-30) REVERT: L 313 MET cc_start: 0.8612 (tpp) cc_final: 0.8338 (ttt) REVERT: L 379 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8496 (t80) REVERT: L 389 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6972 (mp) REVERT: L 400 ASP cc_start: 0.8490 (m-30) cc_final: 0.8120 (t0) REVERT: L 430 PHE cc_start: 0.8775 (m-80) cc_final: 0.8461 (m-80) REVERT: M 215 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.5562 (pmm) REVERT: M 325 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7343 (t80) REVERT: M 481 TYR cc_start: 0.7619 (t80) cc_final: 0.7347 (t80) REVERT: N 30 TRP cc_start: 0.7699 (t-100) cc_final: 0.7177 (t60) REVERT: N 379 MET cc_start: 0.8239 (mmt) cc_final: 0.7887 (mmt) REVERT: N 485 MET cc_start: 0.2325 (mmm) cc_final: 0.2079 (mmm) REVERT: J 85 ARG cc_start: 0.5206 (tpt90) cc_final: 0.4616 (tpt-90) REVERT: J 91 GLN cc_start: 0.6124 (mp10) cc_final: 0.5390 (pm20) REVERT: J 152 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (tt) outliers start: 95 outliers final: 54 residues processed: 585 average time/residue: 0.2136 time to fit residues: 207.8791 Evaluate side-chains 547 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 487 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 462 optimal weight: 0.0870 chunk 345 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 424 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 GLN G 261 HIS B 111 GLN B 116 GLN H 208 HIS N 404 GLN K 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077211 restraints weight = 72019.397| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 0.95 r_work: 0.3019 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38752 Z= 0.396 Angle : 2.483 50.843 52630 Z= 1.428 Chirality : 0.439 6.426 5859 Planarity : 0.004 0.076 6577 Dihedral : 6.634 169.286 5498 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.98 % Allowed : 15.07 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.47 (0.12), residues: 4738 helix: 1.32 (0.10), residues: 2662 sheet: -0.76 (0.29), residues: 322 loop : -1.02 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 86 TYR 0.025 0.002 TYR M 435 PHE 0.029 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01147 / 0.39 (38716) covalent geometry : angle 2.16620 / 1.43 (52537) hydrogen bonds : bond 0.04676 / 3.08 ( 1704) hydrogen bonds : angle 4.10882 / 2.94 ( 5112) metal coordination : bond 0.03418 / 2.17 ( 36) metal coordination : angle 28.94953 / 20.04 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 508 time to evaluate : 1.782 Fit side-chains REVERT: G 583 ASN cc_start: 0.7877 (m-40) cc_final: 0.7567 (t0) REVERT: C 127 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8449 (t80) REVERT: C 284 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: B 94 ASP cc_start: 0.7201 (m-30) cc_final: 0.6433 (t0) REVERT: H 43 PHE cc_start: 0.8456 (m-80) cc_final: 0.8208 (m-80) REVERT: H 229 TYR cc_start: 0.8850 (m-80) cc_final: 0.8278 (m-80) REVERT: L 51 ASP cc_start: 0.8361 (t0) cc_final: 0.7939 (t0) REVERT: L 275 MET cc_start: 0.8545 (mtm) cc_final: 0.8212 (mtm) REVERT: L 354 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6854 (mm) REVERT: L 379 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8435 (t80) REVERT: L 389 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6851 (mp) REVERT: L 400 ASP cc_start: 0.8490 (m-30) cc_final: 0.8123 (t0) REVERT: L 430 PHE cc_start: 0.8789 (m-80) cc_final: 0.8403 (m-80) REVERT: M 325 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7279 (t80) REVERT: M 481 TYR cc_start: 0.7606 (t80) cc_final: 0.7311 (t80) REVERT: N 30 TRP cc_start: 0.7548 (t-100) cc_final: 0.7085 (t60) REVERT: N 379 MET cc_start: 0.8296 (mmt) cc_final: 0.8024 (mmt) REVERT: J 85 ARG cc_start: 0.5323 (tpt90) cc_final: 0.4754 (tpt-90) REVERT: J 91 GLN cc_start: 0.6191 (mp10) cc_final: 0.5469 (pm20) REVERT: J 152 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8238 (tt) outliers start: 116 outliers final: 76 residues processed: 588 average time/residue: 0.2052 time to fit residues: 201.4347 Evaluate side-chains 556 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 473 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 389 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 397 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 351 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 422 ASN B 116 GLN H 214 GLN N 404 GLN K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076143 restraints weight = 72871.136| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 0.91 r_work: 0.2996 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38752 Z= 0.401 Angle : 2.487 50.801 52630 Z= 1.429 Chirality : 0.439 6.428 5859 Planarity : 0.004 0.074 6577 Dihedral : 6.710 169.604 5498 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 3.52 % Allowed : 15.43 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.56 (0.12), residues: 4738 helix: 1.38 (0.10), residues: 2670 sheet: -0.79 (0.29), residues: 321 loop : -0.96 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 804 TYR 0.023 0.002 TYR L 189 PHE 0.029 0.001 PHE L 341 TRP 0.015 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01157 / 0.40 (38716) covalent geometry : angle 2.16951 / 1.43 (52537) hydrogen bonds : bond 0.04801 / 3.15 ( 1704) hydrogen bonds : angle 4.12708 / 2.95 ( 5112) metal coordination : bond 0.02967 / 1.89 ( 36) metal coordination : angle 29.02003 / 20.09 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 491 time to evaluate : 1.114 Fit side-chains REVERT: F 161 MET cc_start: 0.6852 (tpt) cc_final: 0.6511 (tpt) REVERT: F 214 THR cc_start: 0.8524 (m) cc_final: 0.8309 (t) REVERT: G 583 ASN cc_start: 0.7901 (m-40) cc_final: 0.7596 (t0) REVERT: C 127 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8467 (t80) REVERT: B 94 ASP cc_start: 0.7236 (m-30) cc_final: 0.6492 (t0) REVERT: H 43 PHE cc_start: 0.8499 (m-80) cc_final: 0.8225 (m-80) REVERT: L 51 ASP cc_start: 0.8399 (t0) cc_final: 0.7932 (t0) REVERT: L 253 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (mp) REVERT: L 379 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8433 (t80) REVERT: L 389 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6840 (mp) REVERT: L 400 ASP cc_start: 0.8543 (m-30) cc_final: 0.8161 (t0) REVERT: M 325 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7289 (t80) REVERT: M 481 TYR cc_start: 0.7650 (t80) cc_final: 0.7415 (t80) REVERT: N 30 TRP cc_start: 0.7579 (t-100) cc_final: 0.7127 (t60) REVERT: N 379 MET cc_start: 0.8314 (mmt) cc_final: 0.8068 (mmt) REVERT: J 85 ARG cc_start: 0.5346 (tpt90) cc_final: 0.4807 (tpt-90) REVERT: J 91 GLN cc_start: 0.6270 (mp10) cc_final: 0.5593 (pm20) REVERT: J 152 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8219 (tt) outliers start: 137 outliers final: 94 residues processed: 590 average time/residue: 0.1990 time to fit residues: 197.8933 Evaluate side-chains 571 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 471 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 341 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 116 GLN H 208 HIS L 315 GLN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075055 restraints weight = 72861.853| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 0.97 r_work: 0.2968 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38752 Z= 0.410 Angle : 2.494 50.818 52630 Z= 1.432 Chirality : 0.439 6.433 5859 Planarity : 0.004 0.073 6577 Dihedral : 6.915 170.250 5498 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 3.62 % Allowed : 15.99 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.53 (0.12), residues: 4738 helix: 1.36 (0.10), residues: 2664 sheet: -0.79 (0.28), residues: 330 loop : -0.97 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 86 TYR 0.026 0.002 TYR L 189 PHE 0.033 0.002 PHE J 156 TRP 0.013 0.001 TRP C 386 HIS 0.005 0.001 HIS G 709 Details of bonding type rmsd/Z covalent geometry : bond 0.01175 / 0.41 (38716) covalent geometry : angle 2.17572 / 1.43 (52537) hydrogen bonds : bond 0.05063 / 3.32 ( 1704) hydrogen bonds : angle 4.21606 / 3.01 ( 5112) metal coordination : bond 0.03004 / 1.89 ( 36) metal coordination : angle 29.07713 / 20.13 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 495 time to evaluate : 1.103 Fit side-chains REVERT: F 161 MET cc_start: 0.7170 (tpt) cc_final: 0.6917 (tpt) REVERT: F 214 THR cc_start: 0.8591 (m) cc_final: 0.8374 (t) REVERT: F 344 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7194 (mm-30) REVERT: G 583 ASN cc_start: 0.7867 (m-40) cc_final: 0.7546 (t0) REVERT: C 127 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8488 (t80) REVERT: C 284 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: C 571 GLN cc_start: 0.8817 (tt0) cc_final: 0.8585 (tt0) REVERT: B 94 ASP cc_start: 0.7234 (m-30) cc_final: 0.6512 (t70) REVERT: B 170 MET cc_start: 0.7843 (mtp) cc_final: 0.7514 (mtm) REVERT: H 128 TYR cc_start: 0.8128 (m-80) cc_final: 0.7863 (m-80) REVERT: L 51 ASP cc_start: 0.8478 (t0) cc_final: 0.7949 (t0) REVERT: L 253 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (mp) REVERT: L 275 MET cc_start: 0.8598 (mtm) cc_final: 0.8299 (mtm) REVERT: L 379 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (t80) REVERT: L 389 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6838 (mp) REVERT: L 400 ASP cc_start: 0.8581 (m-30) cc_final: 0.8175 (t0) REVERT: L 424 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7919 (mmt) REVERT: M 325 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7394 (t80) REVERT: M 481 TYR cc_start: 0.7699 (t80) cc_final: 0.7491 (t80) REVERT: N 30 TRP cc_start: 0.7646 (t-100) cc_final: 0.7165 (t60) REVERT: N 379 MET cc_start: 0.8311 (mmt) cc_final: 0.8010 (mmp) REVERT: J 85 ARG cc_start: 0.5411 (tpt90) cc_final: 0.4917 (tpt-90) REVERT: J 91 GLN cc_start: 0.6237 (mp10) cc_final: 0.5637 (pm20) REVERT: J 152 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8335 (tt) outliers start: 141 outliers final: 99 residues processed: 594 average time/residue: 0.2060 time to fit residues: 206.6691 Evaluate side-chains 581 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 474 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 291 GLN Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 138 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 466 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 409 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN B 116 GLN H 208 HIS L 236 GLN N 404 GLN K 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076971 restraints weight = 72595.542| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 0.97 r_work: 0.3011 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38752 Z= 0.386 Angle : 2.483 50.817 52630 Z= 1.426 Chirality : 0.438 6.417 5859 Planarity : 0.004 0.073 6577 Dihedral : 6.625 169.503 5498 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.54 % Allowed : 17.30 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.76 (0.12), residues: 4738 helix: 1.55 (0.10), residues: 2667 sheet: -0.76 (0.29), residues: 326 loop : -0.86 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 86 TYR 0.026 0.001 TYR M 435 PHE 0.032 0.001 PHE J 156 TRP 0.012 0.001 TRP G 757 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.39 (38716) covalent geometry : angle 2.16198 / 1.42 (52537) hydrogen bonds : bond 0.04499 / 2.96 ( 1704) hydrogen bonds : angle 4.04539 / 2.89 ( 5112) metal coordination : bond 0.02405 / 1.57 ( 36) metal coordination : angle 29.11054 / 20.26 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 513 time to evaluate : 1.259 Fit side-chains REVERT: F 214 THR cc_start: 0.8621 (m) cc_final: 0.8383 (t) REVERT: G 583 ASN cc_start: 0.7812 (m-40) cc_final: 0.7500 (t0) REVERT: G 750 ARG cc_start: 0.8516 (ptt90) cc_final: 0.8283 (ptt-90) REVERT: C 127 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8529 (t80) REVERT: C 206 MET cc_start: 0.6983 (mmm) cc_final: 0.6624 (mmm) REVERT: C 284 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: C 571 GLN cc_start: 0.8780 (tt0) cc_final: 0.8548 (tt0) REVERT: B 72 PHE cc_start: 0.7552 (m-80) cc_final: 0.7260 (m-80) REVERT: B 94 ASP cc_start: 0.7225 (m-30) cc_final: 0.6453 (t70) REVERT: B 170 MET cc_start: 0.7706 (mtp) cc_final: 0.7437 (mtm) REVERT: H 282 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: L 51 ASP cc_start: 0.8400 (t0) cc_final: 0.7869 (t0) REVERT: L 253 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8730 (mp) REVERT: L 313 MET cc_start: 0.8141 (ttt) cc_final: 0.7899 (ttt) REVERT: L 379 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8449 (t80) REVERT: L 389 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6820 (mp) REVERT: L 400 ASP cc_start: 0.8540 (m-30) cc_final: 0.8146 (t0) REVERT: M 325 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7207 (t80) REVERT: M 481 TYR cc_start: 0.7661 (t80) cc_final: 0.7443 (t80) REVERT: N 30 TRP cc_start: 0.7521 (t-100) cc_final: 0.7083 (t60) REVERT: N 379 MET cc_start: 0.8254 (mmt) cc_final: 0.7991 (mmp) REVERT: J 85 ARG cc_start: 0.5435 (tpt90) cc_final: 0.4812 (tpt-90) REVERT: J 91 GLN cc_start: 0.6157 (mp10) cc_final: 0.5538 (pm20) REVERT: J 152 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8266 (tt) outliers start: 99 outliers final: 66 residues processed: 582 average time/residue: 0.2083 time to fit residues: 203.1834 Evaluate side-chains 559 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 485 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 352 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 447 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 409 GLN E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN C 568 HIS B 111 GLN B 116 GLN H 312 ASN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073753 restraints weight = 72908.999| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 0.90 r_work: 0.2946 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38752 Z= 0.442 Angle : 2.509 50.888 52630 Z= 1.439 Chirality : 0.440 6.445 5859 Planarity : 0.005 0.074 6577 Dihedral : 7.085 170.679 5498 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 3.49 % Allowed : 16.89 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.45 (0.12), residues: 4738 helix: 1.24 (0.10), residues: 2688 sheet: -0.79 (0.29), residues: 320 loop : -0.93 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 86 TYR 0.025 0.002 TYR H 242 PHE 0.031 0.002 PHE J 156 TRP 0.015 0.002 TRP C 386 HIS 0.006 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.01236 / 0.44 (38716) covalent geometry : angle 2.19425 / 1.44 (52537) hydrogen bonds : bond 0.05516 / 3.62 ( 1704) hydrogen bonds : angle 4.35838 / 3.11 ( 5112) metal coordination : bond 0.03171 / 2.00 ( 36) metal coordination : angle 29.03487 / 20.08 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 486 time to evaluate : 1.512 Fit side-chains REVERT: F 214 THR cc_start: 0.8685 (m) cc_final: 0.8384 (t) REVERT: F 344 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7082 (mm-30) REVERT: G 583 ASN cc_start: 0.7863 (m-40) cc_final: 0.7582 (t0) REVERT: C 127 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8489 (t80) REVERT: C 374 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7397 (mmt90) REVERT: C 555 MET cc_start: 0.8855 (mtt) cc_final: 0.8424 (mtt) REVERT: C 571 GLN cc_start: 0.8809 (tt0) cc_final: 0.8592 (tt0) REVERT: B 94 ASP cc_start: 0.7246 (m-30) cc_final: 0.6531 (t70) REVERT: B 170 MET cc_start: 0.7878 (mtp) cc_final: 0.7485 (mtm) REVERT: H 128 TYR cc_start: 0.8242 (m-80) cc_final: 0.7925 (m-80) REVERT: H 312 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8202 (t0) REVERT: L 51 ASP cc_start: 0.8498 (t0) cc_final: 0.7956 (t0) REVERT: L 189 TYR cc_start: 0.9006 (t80) cc_final: 0.8625 (t80) REVERT: L 253 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (mp) REVERT: L 275 MET cc_start: 0.8640 (mtm) cc_final: 0.8408 (mtm) REVERT: L 379 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8502 (t80) REVERT: L 389 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6834 (mp) REVERT: L 400 ASP cc_start: 0.8589 (m-30) cc_final: 0.8169 (t0) REVERT: M 325 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7474 (t80) REVERT: N 30 TRP cc_start: 0.7627 (t-100) cc_final: 0.7144 (t60) REVERT: N 379 MET cc_start: 0.8273 (mmt) cc_final: 0.8040 (mmt) REVERT: J 85 ARG cc_start: 0.5412 (tpt90) cc_final: 0.4794 (tpt-90) REVERT: J 91 GLN cc_start: 0.6118 (mp10) cc_final: 0.5662 (pm20) REVERT: J 152 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (tt) outliers start: 136 outliers final: 102 residues processed: 588 average time/residue: 0.2099 time to fit residues: 207.2793 Evaluate side-chains 582 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 472 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 291 GLN Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 141 optimal weight: 10.0000 chunk 393 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN G 855 ASN B 116 GLN H 208 HIS ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074887 restraints weight = 72328.577| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.99 r_work: 0.2964 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38752 Z= 0.403 Angle : 2.495 50.824 52630 Z= 1.432 Chirality : 0.439 6.426 5859 Planarity : 0.004 0.074 6577 Dihedral : 6.933 170.665 5498 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.06 % Allowed : 17.74 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.56 (0.12), residues: 4738 helix: 1.37 (0.10), residues: 2674 sheet: -0.88 (0.29), residues: 326 loop : -0.90 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 86 TYR 0.022 0.002 TYR M 435 PHE 0.035 0.002 PHE J 156 TRP 0.012 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01161 / 0.40 (38716) covalent geometry : angle 2.17719 / 1.43 (52537) hydrogen bonds : bond 0.05044 / 3.32 ( 1704) hydrogen bonds : angle 4.24684 / 3.03 ( 5112) metal coordination : bond 0.02693 / 1.72 ( 36) metal coordination : angle 29.06034 / 20.16 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 477 time to evaluate : 1.391 Fit side-chains REVERT: F 126 TYR cc_start: 0.8472 (p90) cc_final: 0.8130 (p90) REVERT: F 214 THR cc_start: 0.8679 (m) cc_final: 0.8412 (t) REVERT: F 344 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7172 (mm-30) REVERT: G 583 ASN cc_start: 0.7862 (m-40) cc_final: 0.7545 (t0) REVERT: C 127 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8511 (t80) REVERT: C 206 MET cc_start: 0.6965 (mmm) cc_final: 0.6458 (mmm) REVERT: C 284 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: C 374 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7414 (mmt90) REVERT: C 571 GLN cc_start: 0.8742 (tt0) cc_final: 0.8522 (tt0) REVERT: B 94 ASP cc_start: 0.7263 (m-30) cc_final: 0.6570 (t70) REVERT: B 170 MET cc_start: 0.7882 (mtp) cc_final: 0.7552 (mtm) REVERT: L 51 ASP cc_start: 0.8493 (t0) cc_final: 0.7948 (t0) REVERT: L 253 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8746 (mp) REVERT: L 275 MET cc_start: 0.8598 (mtm) cc_final: 0.8313 (mtm) REVERT: L 379 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8517 (t80) REVERT: L 389 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6845 (mp) REVERT: L 400 ASP cc_start: 0.8592 (m-30) cc_final: 0.8171 (t0) REVERT: M 325 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7394 (t80) REVERT: N 30 TRP cc_start: 0.7578 (t-100) cc_final: 0.7120 (t60) REVERT: N 102 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8579 (mttt) REVERT: N 379 MET cc_start: 0.8290 (mmt) cc_final: 0.8056 (mmt) REVERT: J 85 ARG cc_start: 0.5322 (tpt90) cc_final: 0.5056 (tpt-90) REVERT: J 91 GLN cc_start: 0.6057 (mp10) cc_final: 0.5599 (pm20) REVERT: J 152 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8289 (tt) outliers start: 119 outliers final: 91 residues processed: 565 average time/residue: 0.2009 time to fit residues: 190.8211 Evaluate side-chains 570 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 470 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 SER 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 20 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 273 optimal weight: 6.9990 chunk 316 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 408 optimal weight: 7.9990 chunk 400 optimal weight: 0.9990 chunk 461 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 409 GLN E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN B 116 GLN H 208 HIS N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078055 restraints weight = 73053.947| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 0.95 r_work: 0.3033 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38752 Z= 0.382 Angle : 2.484 50.795 52630 Z= 1.427 Chirality : 0.438 6.415 5859 Planarity : 0.004 0.072 6577 Dihedral : 6.511 168.734 5498 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.11 % Allowed : 18.66 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.86 (0.12), residues: 4738 helix: 1.62 (0.10), residues: 2663 sheet: -0.67 (0.29), residues: 322 loop : -0.79 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 86 TYR 0.029 0.001 TYR M 435 PHE 0.031 0.001 PHE L 341 TRP 0.019 0.001 TRP M 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.38 (38716) covalent geometry : angle 2.16318 / 1.42 (52537) hydrogen bonds : bond 0.04315 / 2.86 ( 1704) hydrogen bonds : angle 4.01174 / 2.87 ( 5112) metal coordination : bond 0.02064 / 1.39 ( 36) metal coordination : angle 29.14163 / 20.34 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 513 time to evaluate : 1.421 Fit side-chains REVERT: F 126 TYR cc_start: 0.8482 (p90) cc_final: 0.8151 (p90) REVERT: F 177 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7919 (tpp80) REVERT: F 214 THR cc_start: 0.8658 (m) cc_final: 0.8429 (t) REVERT: G 869 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7258 (p) REVERT: C 127 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (t80) REVERT: C 206 MET cc_start: 0.6943 (mmm) cc_final: 0.6282 (mmm) REVERT: C 284 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: C 374 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7142 (mmt90) REVERT: C 571 GLN cc_start: 0.8710 (tt0) cc_final: 0.8484 (tt0) REVERT: B 94 ASP cc_start: 0.7230 (m-30) cc_final: 0.6454 (t70) REVERT: B 170 MET cc_start: 0.7666 (mtp) cc_final: 0.7372 (mtm) REVERT: H 43 PHE cc_start: 0.8342 (m-80) cc_final: 0.7977 (m-80) REVERT: H 229 TYR cc_start: 0.8820 (m-80) cc_final: 0.8304 (m-80) REVERT: H 282 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: L 51 ASP cc_start: 0.8414 (t0) cc_final: 0.7898 (t0) REVERT: L 121 ASN cc_start: 0.8531 (m110) cc_final: 0.8243 (m110) REVERT: L 127 MET cc_start: 0.8875 (tpt) cc_final: 0.8551 (tpt) REVERT: L 253 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8696 (mp) REVERT: L 275 MET cc_start: 0.8497 (mtm) cc_final: 0.8275 (mtm) REVERT: L 379 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8348 (t80) REVERT: L 400 ASP cc_start: 0.8532 (m-30) cc_final: 0.8147 (t0) REVERT: M 325 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7149 (t80) REVERT: M 481 TYR cc_start: 0.7756 (t80) cc_final: 0.7346 (t80) REVERT: N 30 TRP cc_start: 0.7464 (t-100) cc_final: 0.7064 (t60) REVERT: N 102 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8508 (mttt) REVERT: N 200 GLU cc_start: 0.6399 (tt0) cc_final: 0.6135 (tt0) REVERT: N 368 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6562 (p-80) REVERT: N 379 MET cc_start: 0.8261 (mmt) cc_final: 0.8004 (mmp) REVERT: J 1 MET cc_start: 0.7059 (tmm) cc_final: 0.6787 (tmm) REVERT: J 85 ARG cc_start: 0.5354 (tpt90) cc_final: 0.5095 (tpt-90) outliers start: 82 outliers final: 69 residues processed: 570 average time/residue: 0.2032 time to fit residues: 193.2246 Evaluate side-chains 562 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 483 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 110 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 425 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 162 optimal weight: 0.2980 chunk 361 optimal weight: 6.9990 chunk 402 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN C 283 ASN B 111 GLN B 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076264 restraints weight = 72363.607| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 0.95 r_work: 0.3000 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38752 Z= 0.395 Angle : 2.491 50.803 52630 Z= 1.430 Chirality : 0.438 6.421 5859 Planarity : 0.004 0.073 6577 Dihedral : 6.626 169.547 5498 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 18.95 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.80 (0.12), residues: 4738 helix: 1.55 (0.10), residues: 2672 sheet: -0.78 (0.29), residues: 330 loop : -0.78 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 86 TYR 0.023 0.002 TYR L 428 PHE 0.030 0.001 PHE J 156 TRP 0.013 0.001 TRP A 125 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.01147 / 0.39 (38716) covalent geometry : angle 2.17230 / 1.43 (52537) hydrogen bonds : bond 0.04692 / 3.09 ( 1704) hydrogen bonds : angle 4.09926 / 2.93 ( 5112) metal coordination : bond 0.02469 / 1.61 ( 36) metal coordination : angle 29.06172 / 20.21 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 482 time to evaluate : 1.296 Fit side-chains REVERT: F 126 TYR cc_start: 0.8473 (p90) cc_final: 0.8171 (p90) REVERT: F 177 ARG cc_start: 0.8296 (tpp-160) cc_final: 0.7990 (tpp80) REVERT: F 214 THR cc_start: 0.8691 (m) cc_final: 0.8406 (t) REVERT: G 797 TYR cc_start: 0.8413 (m-80) cc_final: 0.8104 (m-80) REVERT: G 869 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7320 (p) REVERT: C 127 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8510 (t80) REVERT: C 206 MET cc_start: 0.6968 (mmm) cc_final: 0.6427 (mmm) REVERT: C 374 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7193 (mmt90) REVERT: C 571 GLN cc_start: 0.8756 (tt0) cc_final: 0.8540 (tt0) REVERT: B 94 ASP cc_start: 0.7264 (m-30) cc_final: 0.6506 (t70) REVERT: B 170 MET cc_start: 0.7790 (mtp) cc_final: 0.7441 (mtm) REVERT: H 229 TYR cc_start: 0.8799 (m-80) cc_final: 0.8213 (m-80) REVERT: L 51 ASP cc_start: 0.8416 (t0) cc_final: 0.7873 (t0) REVERT: L 121 ASN cc_start: 0.8554 (m110) cc_final: 0.8261 (m110) REVERT: L 253 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8691 (mp) REVERT: L 379 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8502 (t80) REVERT: L 400 ASP cc_start: 0.8560 (m-30) cc_final: 0.8163 (t0) REVERT: M 325 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7266 (t80) REVERT: M 481 TYR cc_start: 0.7788 (t80) cc_final: 0.7432 (t80) REVERT: N 30 TRP cc_start: 0.7514 (t-100) cc_final: 0.7074 (t60) REVERT: N 102 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8506 (mttt) REVERT: N 200 GLU cc_start: 0.6353 (tt0) cc_final: 0.6147 (tt0) REVERT: N 379 MET cc_start: 0.8258 (mmt) cc_final: 0.8015 (mmt) REVERT: K 86 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7340 (mtp-110) REVERT: J 85 ARG cc_start: 0.5248 (tpt90) cc_final: 0.5008 (tpt-90) outliers start: 81 outliers final: 70 residues processed: 541 average time/residue: 0.2128 time to fit residues: 191.8018 Evaluate side-chains 555 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 478 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 295 optimal weight: 30.0000 chunk 102 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 465 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 457 optimal weight: 0.6980 chunk 444 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 446 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 409 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN C 87 HIS B 116 GLN H 208 HIS ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.074662 restraints weight = 72570.445| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 0.98 r_work: 0.2960 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38752 Z= 0.415 Angle : 2.501 50.819 52630 Z= 1.435 Chirality : 0.439 6.433 5859 Planarity : 0.004 0.073 6577 Dihedral : 6.943 170.720 5498 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.49 % Allowed : 18.64 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.63 (0.12), residues: 4738 helix: 1.41 (0.10), residues: 2677 sheet: -0.88 (0.29), residues: 331 loop : -0.85 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 86 TYR 0.034 0.002 TYR L 189 PHE 0.036 0.002 PHE J 156 TRP 0.013 0.001 TRP L 65 HIS 0.005 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.01185 / 0.42 (38716) covalent geometry : angle 2.18423 / 1.43 (52537) hydrogen bonds : bond 0.05165 / 3.39 ( 1704) hydrogen bonds : angle 4.26371 / 3.04 ( 5112) metal coordination : bond 0.02808 / 1.79 ( 36) metal coordination : angle 29.05706 / 20.14 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9712.92 seconds wall clock time: 166 minutes 47.59 seconds (10007.59 seconds total)