Starting phenix.real_space_refine on Thu Nov 20 19:00:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_13216.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_13216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_13216.map" model { file = "/net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_13216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p63_13216/11_2025/7p63_13216.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 8.56, per 1000 atoms: 0.23 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: 3.59 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="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: 1.02 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: 6.57 Time building geometry restraints manager: 4.65 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=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.607 0.069 2.00e-02 2.50e+03 1.19e+01 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 ... (remaining 38711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 51571 2.42 - 4.85: 785 4.85 - 7.27: 134 7.27 - 9.69: 36 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 - 22.74: 20980 22.74 - 45.49: 1572 45.49 - 68.23: 228 68.23 - 90.98: 37 90.98 - 113.72: 6 Dihedral angle restraints: 22823 sinusoidal: 9190 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=" CA MET J 73 " pdb=" C MET J 73 " pdb=" N LEU J 74 " pdb=" CA LEU J 74 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 22820 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: 6578 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 6575 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: 0.540 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: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.610 Find NCS groups from input model: 0.230 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 0.099 38752 Z= 0.211 Angle : 0.786 15.696 52630 Z= 0.394 Chirality : 1.461 21.215 5859 Planarity : 0.006 0.121 6578 Dihedral : 15.665 113.720 14105 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 covalent geometry : bond 0.00442 (38716) covalent geometry : angle 0.77051 (52537) hydrogen bonds : bond 0.05110 ( 1704) hydrogen bonds : angle 4.69403 ( 5112) metal coordination : bond 0.05438 ( 36) metal coordination : angle 3.77518 ( 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 : 1.523 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: 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: 0.2501 time to fit residues: 230.6495 Evaluate side-chains 508 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 501 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 304 HIS ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN C 135 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077709 restraints weight = 72340.372| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 0.95 r_work: 0.3025 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.265 38752 Z= 0.410 Angle : 2.492 51.071 52630 Z= 1.431 Chirality : 0.438 6.481 5859 Planarity : 0.005 0.081 6578 Dihedral : 8.605 104.728 5658 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 2.41 % Allowed : 14.89 % Favored : 82.70 % 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: 0.13 (0.12), residues: 4738 helix: 1.00 (0.10), residues: 2674 sheet: -0.78 (0.28), residues: 325 loop : -1.12 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 320 TYR 0.025 0.002 TYR M 435 PHE 0.028 0.002 PHE L 341 TRP 0.015 0.001 TRP F 353 HIS 0.006 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.01179 (38716) covalent geometry : angle 2.17459 (52537) hydrogen bonds : bond 0.04827 ( 1704) hydrogen bonds : angle 4.19316 ( 5112) metal coordination : bond 0.03844 ( 36) metal coordination : angle 29.03685 ( 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 611 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 517 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: F 161 MET cc_start: 0.6409 (tpt) cc_final: 0.6064 (tpt) REVERT: G 150 MET cc_start: 0.8895 (tpp) cc_final: 0.8636 (tpp) REVERT: G 583 ASN cc_start: 0.7868 (m-40) cc_final: 0.7544 (t0) REVERT: G 901 HIS cc_start: 0.7358 (m-70) cc_final: 0.7140 (m-70) REVERT: C 127 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8343 (t80) REVERT: C 206 MET cc_start: 0.7326 (mmm) cc_final: 0.7073 (mmm) REVERT: B 94 ASP cc_start: 0.7244 (m-30) cc_final: 0.6424 (t0) REVERT: H 31 PHE cc_start: 0.6307 (m-10) cc_final: 0.6063 (m-10) REVERT: A 62 LEU cc_start: 0.5234 (mp) cc_final: 0.5015 (mp) REVERT: L 144 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7351 (mm-30) REVERT: L 253 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8701 (mp) REVERT: L 313 MET cc_start: 0.8635 (tpp) cc_final: 0.8379 (ttt) REVERT: L 379 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (t80) REVERT: L 389 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6983 (mp) REVERT: L 400 ASP cc_start: 0.8506 (m-30) cc_final: 0.8129 (t0) REVERT: L 430 PHE cc_start: 0.8778 (m-80) cc_final: 0.8460 (m-80) REVERT: M 215 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.5551 (pmm) REVERT: M 325 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7346 (t80) REVERT: M 481 TYR cc_start: 0.7633 (t80) cc_final: 0.7355 (t80) REVERT: N 30 TRP cc_start: 0.7707 (t-100) cc_final: 0.7179 (t60) REVERT: N 379 MET cc_start: 0.8232 (mmt) cc_final: 0.7842 (mmt) REVERT: N 485 MET cc_start: 0.2193 (mmm) cc_final: 0.1951 (mmm) REVERT: J 85 ARG cc_start: 0.5205 (tpt90) cc_final: 0.4617 (tpt-90) REVERT: J 91 GLN cc_start: 0.6125 (mp10) cc_final: 0.5387 (pm20) REVERT: J 152 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (tt) outliers start: 94 outliers final: 53 residues processed: 582 average time/residue: 0.2402 time to fit residues: 232.4695 Evaluate side-chains 542 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 482 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 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 371 MET Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 139 LEU 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: 8.9990 chunk 92 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 462 optimal weight: 3.9990 chunk 345 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN G 261 HIS ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 111 GLN B 116 GLN H 208 HIS N 404 GLN K 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077665 restraints weight = 72060.738| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 0.96 r_work: 0.3022 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1107 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= 0.394 Angle : 2.482 50.811 52630 Z= 1.427 Chirality : 0.439 6.431 5859 Planarity : 0.004 0.076 6578 Dihedral : 8.330 98.948 5648 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 2.77 % Allowed : 15.15 % Favored : 82.08 % 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: 2661 sheet: -0.76 (0.29), residues: 322 loop : -1.03 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 369 TYR 0.025 0.001 TYR M 435 PHE 0.029 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01144 (38716) covalent geometry : angle 2.16496 (52537) hydrogen bonds : bond 0.04629 ( 1704) hydrogen bonds : angle 4.09918 ( 5112) metal coordination : bond 0.03295 ( 36) metal coordination : angle 28.95190 ( 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 618 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 510 time to evaluate : 1.528 Fit side-chains REVERT: G 583 ASN cc_start: 0.7895 (m-40) cc_final: 0.7581 (t0) REVERT: C 127 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8413 (t80) REVERT: B 94 ASP cc_start: 0.7219 (m-30) cc_final: 0.6449 (t0) REVERT: H 31 PHE cc_start: 0.6314 (m-10) cc_final: 0.6082 (m-10) REVERT: H 43 PHE cc_start: 0.8419 (m-80) cc_final: 0.8157 (m-80) REVERT: L 51 ASP cc_start: 0.8382 (t0) cc_final: 0.7976 (t0) REVERT: L 253 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8726 (mp) REVERT: L 275 MET cc_start: 0.8526 (mtm) cc_final: 0.8196 (mtm) REVERT: L 379 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8492 (t80) REVERT: L 389 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6946 (mp) REVERT: L 400 ASP cc_start: 0.8502 (m-30) cc_final: 0.8134 (t0) REVERT: L 430 PHE cc_start: 0.8785 (m-80) cc_final: 0.8398 (m-80) REVERT: M 325 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7309 (t80) REVERT: M 481 TYR cc_start: 0.7601 (t80) cc_final: 0.7307 (t80) REVERT: N 30 TRP cc_start: 0.7559 (t-100) cc_final: 0.7097 (t60) REVERT: N 43 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8645 (mp) REVERT: N 379 MET cc_start: 0.8306 (mmt) cc_final: 0.8033 (mmt) REVERT: N 485 MET cc_start: 0.2248 (mmm) cc_final: 0.2018 (mmm) REVERT: J 85 ARG cc_start: 0.5315 (tpt90) cc_final: 0.4914 (tpt-90) REVERT: J 91 GLN cc_start: 0.6186 (mp10) cc_final: 0.5459 (pm20) REVERT: J 152 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8259 (tt) outliers start: 108 outliers final: 71 residues processed: 583 average time/residue: 0.2450 time to fit residues: 238.0105 Evaluate side-chains 554 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 476 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 43 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 128 LEU 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: 1.9990 chunk 176 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 351 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 422 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 116 GLN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3266 r_free = 0.3266 target = 0.086642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077072 restraints weight = 72836.212| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.01 r_work: 0.3004 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38752 Z= 0.391 Angle : 2.481 50.818 52630 Z= 1.427 Chirality : 0.438 6.418 5859 Planarity : 0.004 0.074 6578 Dihedral : 8.089 94.798 5648 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.21 % Allowed : 15.58 % Favored : 81.21 % 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: 1.46 (0.10), residues: 2660 sheet: -0.77 (0.29), residues: 323 loop : -0.95 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 804 TYR 0.025 0.001 TYR L 189 PHE 0.032 0.001 PHE J 156 TRP 0.017 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01140 (38716) covalent geometry : angle 2.16349 (52537) hydrogen bonds : bond 0.04560 ( 1704) hydrogen bonds : angle 4.05134 ( 5112) metal coordination : bond 0.02800 ( 36) metal coordination : angle 28.97176 ( 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 622 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 497 time to evaluate : 1.504 Fit side-chains REVERT: F 161 MET cc_start: 0.6752 (tpt) cc_final: 0.6384 (tpt) REVERT: G 583 ASN cc_start: 0.7934 (m-40) cc_final: 0.7599 (t0) REVERT: G 812 TRP cc_start: 0.8880 (m100) cc_final: 0.8526 (m100) REVERT: C 127 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8488 (t80) REVERT: C 284 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: B 94 ASP cc_start: 0.7212 (m-30) cc_final: 0.6437 (t0) REVERT: H 43 PHE cc_start: 0.8432 (m-80) cc_final: 0.8125 (m-80) REVERT: H 229 TYR cc_start: 0.8820 (m-80) cc_final: 0.8145 (m-80) REVERT: L 51 ASP cc_start: 0.8410 (t0) cc_final: 0.7943 (t0) REVERT: L 379 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8472 (t80) REVERT: L 389 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6866 (mp) REVERT: L 400 ASP cc_start: 0.8572 (m-30) cc_final: 0.8164 (t0) REVERT: M 325 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7216 (t80) REVERT: M 481 TYR cc_start: 0.7677 (t80) cc_final: 0.7390 (t80) REVERT: N 30 TRP cc_start: 0.7574 (t-100) cc_final: 0.7120 (t60) REVERT: N 43 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8659 (mp) REVERT: N 379 MET cc_start: 0.8343 (mmt) cc_final: 0.8060 (mmt) REVERT: N 485 MET cc_start: 0.2383 (mmm) cc_final: 0.2173 (mmm) REVERT: J 85 ARG cc_start: 0.5313 (tpt90) cc_final: 0.4770 (tpt-90) REVERT: J 91 GLN cc_start: 0.6282 (mp10) cc_final: 0.5620 (pm20) REVERT: J 152 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (tt) outliers start: 125 outliers final: 79 residues processed: 588 average time/residue: 0.2355 time to fit residues: 231.4707 Evaluate side-chains 558 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 472 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG 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 E residue 154 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER 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 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 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 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS 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 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 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 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 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 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 43 ILE 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 174 MET 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 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 341 ASN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 116 GLN H 208 HIS H 312 ASN L 315 GLN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073804 restraints weight = 73018.172| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 0.99 r_work: 0.2943 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38752 Z= 0.441 Angle : 2.506 50.856 52630 Z= 1.438 Chirality : 0.440 6.459 5859 Planarity : 0.005 0.074 6578 Dihedral : 8.496 94.766 5648 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 3.62 % Allowed : 15.92 % Favored : 80.46 % 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: 0.38 (0.12), residues: 4738 helix: 1.20 (0.10), residues: 2685 sheet: -0.78 (0.29), residues: 320 loop : -0.99 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 86 TYR 0.025 0.002 TYR G 711 PHE 0.032 0.002 PHE J 156 TRP 0.015 0.002 TRP C 386 HIS 0.006 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.01234 (38716) covalent geometry : angle 2.19124 (52537) hydrogen bonds : bond 0.05498 ( 1704) hydrogen bonds : angle 4.34703 ( 5112) metal coordination : bond 0.03320 ( 36) metal coordination : angle 29.02525 ( 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 630 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 489 time to evaluate : 1.539 Fit side-chains REVERT: F 161 MET cc_start: 0.7150 (tpt) cc_final: 0.6914 (tpt) REVERT: F 344 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7146 (mm-30) REVERT: G 583 ASN cc_start: 0.7900 (m-40) cc_final: 0.7604 (t0) REVERT: G 745 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: C 127 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (t80) REVERT: C 571 GLN cc_start: 0.8836 (tt0) cc_final: 0.8611 (tt0) REVERT: B 94 ASP cc_start: 0.7258 (m-30) cc_final: 0.6517 (t70) REVERT: B 170 MET cc_start: 0.7808 (mtp) cc_final: 0.7477 (mtm) REVERT: H 312 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8207 (t0) REVERT: L 51 ASP cc_start: 0.8502 (t0) cc_final: 0.7960 (t0) REVERT: L 275 MET cc_start: 0.8674 (mtm) cc_final: 0.8354 (mtm) REVERT: L 379 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8494 (t80) REVERT: L 389 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6838 (mp) REVERT: L 400 ASP cc_start: 0.8611 (m-30) cc_final: 0.8174 (t0) REVERT: M 325 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7435 (t80) REVERT: N 30 TRP cc_start: 0.7683 (t-100) cc_final: 0.7196 (t60) REVERT: N 379 MET cc_start: 0.8290 (mmt) cc_final: 0.8029 (mmt) REVERT: J 91 GLN cc_start: 0.6244 (mp10) cc_final: 0.5627 (pm20) REVERT: J 152 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8231 (tt) outliers start: 141 outliers final: 100 residues processed: 589 average time/residue: 0.2380 time to fit residues: 236.7569 Evaluate side-chains 572 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 465 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 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 745 GLN 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 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 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 153 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL 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 68 PHE Chi-restraints excluded: chain A residue 83 LEU 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 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 L residue 608 LEU 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 229 ILE 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 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 152 SER 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 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: 0.9990 chunk 15 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 466 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 291 optimal weight: 0.3980 chunk 376 optimal weight: 6.9990 chunk 175 optimal weight: 0.3980 chunk 312 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 208 HIS H 214 GLN L 236 GLN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077012 restraints weight = 72458.043| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.01 r_work: 0.3007 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1548 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= 0.384 Angle : 2.482 50.824 52630 Z= 1.426 Chirality : 0.438 6.419 5859 Planarity : 0.004 0.073 6578 Dihedral : 7.958 89.972 5648 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.57 % Allowed : 17.10 % Favored : 80.33 % 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: 0.70 (0.12), residues: 4738 helix: 1.51 (0.10), residues: 2674 sheet: -0.84 (0.29), residues: 325 loop : -0.88 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 86 TYR 0.026 0.001 TYR M 435 PHE 0.037 0.001 PHE L 296 TRP 0.014 0.001 TRP G 757 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01126 (38716) covalent geometry : angle 2.16184 (52537) hydrogen bonds : bond 0.04541 ( 1704) hydrogen bonds : angle 4.07697 ( 5112) metal coordination : bond 0.02295 ( 36) metal coordination : angle 29.09609 ( 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 608 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 508 time to evaluate : 1.531 Fit side-chains REVERT: F 214 THR cc_start: 0.8634 (m) cc_final: 0.8390 (t) REVERT: F 344 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7098 (mm-30) REVERT: G 583 ASN cc_start: 0.7822 (m-40) cc_final: 0.7511 (t0) REVERT: C 127 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8453 (t80) REVERT: C 206 MET cc_start: 0.6940 (mmm) cc_final: 0.6467 (mmm) REVERT: C 284 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: C 571 GLN cc_start: 0.8747 (tt0) cc_final: 0.8515 (tt0) REVERT: B 72 PHE cc_start: 0.7493 (m-80) cc_final: 0.7287 (m-80) REVERT: B 94 ASP cc_start: 0.7182 (m-30) cc_final: 0.6462 (t70) REVERT: B 170 MET cc_start: 0.7720 (mtp) cc_final: 0.7439 (mtm) REVERT: H 216 GLU cc_start: 0.7064 (pm20) cc_final: 0.6681 (pm20) REVERT: H 282 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: L 51 ASP cc_start: 0.8423 (t0) cc_final: 0.7897 (t0) REVERT: L 121 ASN cc_start: 0.8580 (m110) cc_final: 0.8277 (m110) REVERT: L 379 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8441 (t80) REVERT: L 389 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6876 (mp) REVERT: L 400 ASP cc_start: 0.8550 (m-30) cc_final: 0.8156 (t0) REVERT: L 424 MET cc_start: 0.8246 (mmm) cc_final: 0.7815 (mmt) REVERT: M 325 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7240 (t80) REVERT: M 481 TYR cc_start: 0.7769 (t80) cc_final: 0.7485 (t80) REVERT: N 30 TRP cc_start: 0.7530 (t-100) cc_final: 0.7090 (t60) REVERT: N 43 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8627 (mp) REVERT: N 102 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8462 (mttt) REVERT: N 379 MET cc_start: 0.8256 (mmt) cc_final: 0.8035 (mmt) REVERT: N 485 MET cc_start: 0.3014 (mmm) cc_final: 0.2541 (mmm) REVERT: J 85 ARG cc_start: 0.5354 (tpt90) cc_final: 0.4902 (tpt-90) REVERT: J 91 GLN cc_start: 0.6101 (mp10) cc_final: 0.5516 (pm20) REVERT: J 152 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8269 (tt) outliers start: 100 outliers final: 66 residues processed: 579 average time/residue: 0.2323 time to fit residues: 227.4210 Evaluate side-chains 555 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 480 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG 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 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 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 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 6 THR Chi-restraints excluded: chain B residue 63 CYS 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 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 160 ASP 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 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 374 MET 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 43 ILE 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 152 SER Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 46 PHE 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: 0.9990 chunk 95 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 432 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 447 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN E 78 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 116 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3237 r_free = 0.3237 target = 0.085028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075423 restraints weight = 72745.165| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.99 r_work: 0.2975 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1656 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= 0.404 Angle : 2.491 50.793 52630 Z= 1.431 Chirality : 0.439 6.424 5859 Planarity : 0.004 0.073 6578 Dihedral : 7.928 88.651 5648 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.00 % Allowed : 17.10 % Favored : 79.90 % 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: 0.67 (0.12), residues: 4738 helix: 1.47 (0.10), residues: 2667 sheet: -0.82 (0.29), residues: 329 loop : -0.89 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 86 TYR 0.025 0.002 TYR H 242 PHE 0.029 0.002 PHE L 341 TRP 0.011 0.001 TRP G 812 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.01163 (38716) covalent geometry : angle 2.17371 (52537) hydrogen bonds : bond 0.04900 ( 1704) hydrogen bonds : angle 4.17314 ( 5112) metal coordination : bond 0.02751 ( 36) metal coordination : angle 29.03102 ( 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 608 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 491 time to evaluate : 1.583 Fit side-chains REVERT: F 214 THR cc_start: 0.8662 (m) cc_final: 0.8361 (t) REVERT: G 583 ASN cc_start: 0.7856 (m-40) cc_final: 0.7529 (t0) REVERT: G 745 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: C 127 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8475 (t80) REVERT: C 374 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7246 (mmt90) REVERT: C 571 GLN cc_start: 0.8803 (tt0) cc_final: 0.8585 (tt0) REVERT: B 94 ASP cc_start: 0.7270 (m-30) cc_final: 0.6527 (t70) REVERT: B 170 MET cc_start: 0.7826 (mtp) cc_final: 0.7498 (mtm) REVERT: L 51 ASP cc_start: 0.8460 (t0) cc_final: 0.7935 (t0) REVERT: L 253 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8776 (mp) REVERT: L 275 MET cc_start: 0.8605 (mtm) cc_final: 0.8369 (mtm) REVERT: L 299 LEU cc_start: 0.8163 (tp) cc_final: 0.7959 (tp) REVERT: L 379 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8518 (t80) REVERT: L 389 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6830 (mp) REVERT: L 400 ASP cc_start: 0.8568 (m-30) cc_final: 0.8177 (t0) REVERT: M 325 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7352 (t80) REVERT: M 481 TYR cc_start: 0.7730 (t80) cc_final: 0.7462 (t80) REVERT: N 30 TRP cc_start: 0.7599 (t-100) cc_final: 0.7146 (t60) REVERT: N 43 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8637 (mp) REVERT: N 379 MET cc_start: 0.8271 (mmt) cc_final: 0.8037 (mmt) REVERT: N 485 MET cc_start: 0.3041 (mmm) cc_final: 0.2593 (mmm) REVERT: J 85 ARG cc_start: 0.5224 (tpt90) cc_final: 0.4595 (tpt-90) REVERT: J 91 GLN cc_start: 0.6083 (mp10) cc_final: 0.5620 (pm20) REVERT: J 152 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 117 outliers final: 91 residues processed: 580 average time/residue: 0.2294 time to fit residues: 224.6690 Evaluate side-chains 579 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 479 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 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 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 745 GLN 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 115 VAL 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 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 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 71 SER 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 52 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 289 LEU 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 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 43 ILE 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 152 SER Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET 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: 0.3980 chunk 142 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN E 78 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3271 r_free = 0.3271 target = 0.086879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077409 restraints weight = 72307.759| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.01 r_work: 0.3015 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38752 Z= 0.385 Angle : 2.484 50.798 52630 Z= 1.427 Chirality : 0.438 6.414 5859 Planarity : 0.004 0.073 6578 Dihedral : 7.529 87.335 5648 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.49 % Allowed : 18.07 % Favored : 79.44 % 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: 0.83 (0.12), residues: 4738 helix: 1.60 (0.10), residues: 2673 sheet: -0.77 (0.29), residues: 327 loop : -0.80 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 750 TYR 0.025 0.001 TYR M 435 PHE 0.030 0.001 PHE L 341 TRP 0.014 0.001 TRP M 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01128 (38716) covalent geometry : angle 2.16384 (52537) hydrogen bonds : bond 0.04427 ( 1704) hydrogen bonds : angle 4.03751 ( 5112) metal coordination : bond 0.02211 ( 36) metal coordination : angle 29.08671 ( 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 597 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 500 time to evaluate : 1.549 Fit side-chains REVERT: F 126 TYR cc_start: 0.8487 (p90) cc_final: 0.8114 (p90) REVERT: F 214 THR cc_start: 0.8673 (m) cc_final: 0.8414 (t) REVERT: G 583 ASN cc_start: 0.7824 (m-40) cc_final: 0.7492 (t0) REVERT: G 812 TRP cc_start: 0.8726 (m100) cc_final: 0.8446 (m-90) REVERT: G 869 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7282 (p) REVERT: C 127 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8480 (t80) REVERT: C 206 MET cc_start: 0.6939 (mmm) cc_final: 0.6420 (mmm) REVERT: C 284 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: C 374 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7390 (mmt90) REVERT: C 571 GLN cc_start: 0.8740 (tt0) cc_final: 0.8515 (tt0) REVERT: B 94 ASP cc_start: 0.7255 (m-30) cc_final: 0.6463 (t70) REVERT: B 170 MET cc_start: 0.7807 (mtp) cc_final: 0.7437 (mtm) REVERT: H 229 TYR cc_start: 0.8896 (m-80) cc_final: 0.8333 (m-80) REVERT: L 51 ASP cc_start: 0.8416 (t0) cc_final: 0.7847 (t0) REVERT: L 121 ASN cc_start: 0.8531 (m110) cc_final: 0.8240 (m110) REVERT: L 253 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8778 (mp) REVERT: L 275 MET cc_start: 0.8553 (mtm) cc_final: 0.8325 (mtm) REVERT: L 379 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8388 (t80) REVERT: L 389 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6802 (mp) REVERT: L 400 ASP cc_start: 0.8571 (m-30) cc_final: 0.8172 (t0) REVERT: L 424 MET cc_start: 0.8482 (mmt) cc_final: 0.7882 (mmt) REVERT: M 7 ILE cc_start: 0.8516 (mt) cc_final: 0.8301 (mt) REVERT: M 325 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7180 (t80) REVERT: M 481 TYR cc_start: 0.7735 (t80) cc_final: 0.7451 (t80) REVERT: N 30 TRP cc_start: 0.7520 (t-100) cc_final: 0.7073 (t60) REVERT: N 43 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8584 (mp) REVERT: N 102 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8504 (mttt) REVERT: N 379 MET cc_start: 0.8273 (mmt) cc_final: 0.8027 (mmt) REVERT: N 485 MET cc_start: 0.3014 (mmm) cc_final: 0.2572 (mmm) REVERT: J 85 ARG cc_start: 0.5276 (tpt90) cc_final: 0.4675 (tpt-90) REVERT: J 152 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8227 (tt) outliers start: 97 outliers final: 79 residues processed: 571 average time/residue: 0.2348 time to fit residues: 224.1201 Evaluate side-chains 570 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 480 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 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 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 6 THR 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 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 5 SER 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 289 LEU 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 68 MET 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 249 VAL 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 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 43 ILE 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 152 SER Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 46 PHE 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: 9.9990 chunk 316 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 chunk 400 optimal weight: 0.7980 chunk 461 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN G 855 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 116 GLN H 312 ASN 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 = 0.3278 r_free = 0.3278 target = 0.087262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077730 restraints weight = 73145.773| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.00 r_work: 0.3023 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1610 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= 0.384 Angle : 2.483 50.781 52630 Z= 1.427 Chirality : 0.438 6.411 5859 Planarity : 0.004 0.072 6578 Dihedral : 7.339 86.187 5648 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 18.00 % Favored : 79.46 % 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: 0.92 (0.12), residues: 4738 helix: 1.66 (0.10), residues: 2671 sheet: -0.71 (0.29), residues: 332 loop : -0.74 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 86 TYR 0.024 0.001 TYR M 435 PHE 0.030 0.001 PHE L 341 TRP 0.013 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01128 (38716) covalent geometry : angle 2.16306 (52537) hydrogen bonds : bond 0.04334 ( 1704) hydrogen bonds : angle 4.01020 ( 5112) metal coordination : bond 0.02188 ( 36) metal coordination : angle 29.08235 ( 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 599 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 500 time to evaluate : 1.438 Fit side-chains REVERT: F 126 TYR cc_start: 0.8486 (p90) cc_final: 0.8125 (p90) REVERT: F 177 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7881 (tpp80) REVERT: F 214 THR cc_start: 0.8698 (m) cc_final: 0.8407 (t) REVERT: G 812 TRP cc_start: 0.8703 (m100) cc_final: 0.8480 (m-90) REVERT: G 869 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7207 (p) REVERT: C 127 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8499 (t80) REVERT: C 206 MET cc_start: 0.6955 (mmm) cc_final: 0.6416 (mmm) REVERT: C 284 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: C 374 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7381 (mmt90) REVERT: C 566 TYR cc_start: 0.8596 (t80) cc_final: 0.8270 (t80) REVERT: C 571 GLN cc_start: 0.8761 (tt0) cc_final: 0.8552 (tt0) REVERT: B 94 ASP cc_start: 0.7278 (m-30) cc_final: 0.6504 (t70) REVERT: B 170 MET cc_start: 0.7773 (mtp) cc_final: 0.7406 (mtm) REVERT: H 229 TYR cc_start: 0.8831 (m-80) cc_final: 0.8197 (m-80) REVERT: H 312 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8457 (t0) REVERT: L 51 ASP cc_start: 0.8362 (t0) cc_final: 0.7877 (t0) REVERT: L 121 ASN cc_start: 0.8506 (m110) cc_final: 0.8230 (m110) REVERT: L 253 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8764 (mp) REVERT: L 275 MET cc_start: 0.8546 (mtm) cc_final: 0.8308 (mtm) REVERT: L 354 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6714 (mm) REVERT: L 379 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8380 (t80) REVERT: L 389 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6875 (mp) REVERT: L 400 ASP cc_start: 0.8548 (m-30) cc_final: 0.8150 (t0) REVERT: M 7 ILE cc_start: 0.8510 (mt) cc_final: 0.8272 (mt) REVERT: M 175 PHE cc_start: 0.8622 (t80) cc_final: 0.8411 (t80) REVERT: M 325 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7128 (t80) REVERT: M 481 TYR cc_start: 0.7709 (t80) cc_final: 0.7388 (t80) REVERT: N 30 TRP cc_start: 0.7505 (t-100) cc_final: 0.7066 (t60) REVERT: N 43 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8551 (mp) REVERT: N 102 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8499 (mttt) REVERT: N 200 GLU cc_start: 0.6373 (tt0) cc_final: 0.6171 (tt0) REVERT: N 379 MET cc_start: 0.8234 (mmt) cc_final: 0.7959 (mmp) REVERT: N 485 MET cc_start: 0.2916 (mmm) cc_final: 0.2465 (mmm) REVERT: J 2 GLU cc_start: 0.6986 (pm20) cc_final: 0.6765 (tt0) REVERT: J 85 ARG cc_start: 0.5195 (tpt90) cc_final: 0.4916 (tpt-90) outliers start: 99 outliers final: 76 residues processed: 573 average time/residue: 0.2336 time to fit residues: 223.5897 Evaluate side-chains 574 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 486 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 121 THR Chi-restraints excluded: chain E residue 143 MET 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 617 GLU Chi-restraints excluded: chain G residue 618 SER 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 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 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS 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 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 5 SER 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 289 LEU 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 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 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE 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 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 418 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 43 ILE 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 152 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 110 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN L 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074276 restraints weight = 72821.920| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 0.96 r_work: 0.2957 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38752 Z= 0.439 Angle : 2.511 50.861 52630 Z= 1.440 Chirality : 0.440 6.447 5859 Planarity : 0.005 0.075 6578 Dihedral : 7.876 85.696 5648 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 2.75 % Allowed : 17.95 % Favored : 79.31 % 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: 1.33 (0.10), residues: 2679 sheet: -0.77 (0.29), residues: 324 loop : -0.86 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 86 TYR 0.034 0.002 TYR L 189 PHE 0.028 0.002 PHE L 430 TRP 0.019 0.002 TRP M 122 HIS 0.007 0.002 HIS G 709 Details of bonding type rmsd covalent geometry : bond 0.01230 (38716) covalent geometry : angle 2.19584 (52537) hydrogen bonds : bond 0.05389 ( 1704) hydrogen bonds : angle 4.31940 ( 5112) metal coordination : bond 0.03029 ( 36) metal coordination : angle 29.05387 ( 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 585 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 478 time to evaluate : 1.446 Fit side-chains REVERT: F 126 TYR cc_start: 0.8497 (p90) cc_final: 0.8147 (p90) REVERT: F 214 THR cc_start: 0.8695 (m) cc_final: 0.8383 (t) REVERT: C 127 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8498 (t80) REVERT: C 374 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7398 (mmt90) REVERT: C 571 GLN cc_start: 0.8794 (tt0) cc_final: 0.8589 (tt0) REVERT: B 94 ASP cc_start: 0.7224 (m-30) cc_final: 0.6520 (t70) REVERT: B 170 MET cc_start: 0.7832 (mtp) cc_final: 0.7420 (mtm) REVERT: L 51 ASP cc_start: 0.8445 (t0) cc_final: 0.7859 (t0) REVERT: L 253 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8771 (mp) REVERT: L 379 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8501 (t80) REVERT: L 389 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6825 (mp) REVERT: L 400 ASP cc_start: 0.8555 (m-30) cc_final: 0.8145 (t0) REVERT: M 325 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7469 (t80) REVERT: M 481 TYR cc_start: 0.7704 (t80) cc_final: 0.7435 (t80) REVERT: N 30 TRP cc_start: 0.7607 (t-100) cc_final: 0.7126 (t60) REVERT: N 102 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: N 200 GLU cc_start: 0.6319 (tt0) cc_final: 0.6106 (tt0) REVERT: N 379 MET cc_start: 0.8257 (mmt) cc_final: 0.8023 (mmt) REVERT: N 485 MET cc_start: 0.3130 (mmm) cc_final: 0.2766 (mmm) REVERT: J 85 ARG cc_start: 0.5291 (tpt90) cc_final: 0.5005 (tpt-90) REVERT: J 91 GLN cc_start: 0.6043 (mp10) cc_final: 0.5600 (pm20) outliers start: 107 outliers final: 86 residues processed: 559 average time/residue: 0.2284 time to fit residues: 213.1851 Evaluate side-chains 558 residues out of total 3902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 465 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 121 THR Chi-restraints excluded: chain E residue 143 MET 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 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 127 PHE 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 484 CYS 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 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 5 SER 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 289 LEU 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 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 147 LEU Chi-restraints excluded: chain M residue 148 VAL 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 418 VAL 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 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 152 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 295 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 chunk 253 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 457 optimal weight: 20.0000 chunk 444 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 446 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN G 855 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 190 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 = 0.3239 r_free = 0.3239 target = 0.085124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075595 restraints weight = 72719.860| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.00 r_work: 0.2982 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1805 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= 0.397 Angle : 2.494 50.806 52630 Z= 1.432 Chirality : 0.439 6.423 5859 Planarity : 0.004 0.074 6578 Dihedral : 7.694 85.332 5648 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.39 % Allowed : 18.31 % Favored : 79.31 % 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: 0.69 (0.12), residues: 4738 helix: 1.45 (0.10), residues: 2673 sheet: -0.83 (0.29), residues: 335 loop : -0.82 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 86 TYR 0.024 0.002 TYR L 428 PHE 0.036 0.001 PHE J 156 TRP 0.011 0.001 TRP L 65 HIS 0.005 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.01151 (38716) covalent geometry : angle 2.17569 (52537) hydrogen bonds : bond 0.04912 ( 1704) hydrogen bonds : angle 4.20469 ( 5112) metal coordination : bond 0.02551 ( 36) metal coordination : angle 29.08137 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11057.16 seconds wall clock time: 189 minutes 27.50 seconds (11367.50 seconds total)