Starting phenix.real_space_refine on Sat Mar 7 03:24:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7l_13239/03_2026/7p7l_13239.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.017 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 16 5.49 5 S 266 5.16 5 C 24527 2.51 5 N 6162 2.21 5 O 6583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37587 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4705 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 547} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2444 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4498 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain breaks: 2 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: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3630 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 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: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1214 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'SF4': 1, 'UQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UQ8:plan-2': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "L" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'3PE': 5, 'LFA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 73.598 60.094 192.702 1.00 81.30 S ATOM 2741 SG CYS F 357 77.444 59.772 196.893 1.00112.84 S ATOM 2697 SG CYS F 351 75.896 53.793 194.168 1.00160.05 S ATOM 4054 SG CYS E 92 85.692 50.893 213.156 1.00150.77 S ATOM 4088 SG CYS E 97 86.327 51.892 216.566 1.00137.26 S ATOM 5476 SG CYS G 114 83.830 65.896 174.866 1.00 22.18 S ATOM 5416 SG CYS G 105 89.114 69.604 176.256 1.00 22.78 S ATOM 5436 SG CYS G 108 89.729 63.600 173.866 1.00 27.41 S ATOM 5830 SG CYS G 156 77.963 58.252 180.051 1.00 74.70 S ATOM 5811 SG CYS G 153 83.864 57.075 182.836 1.00 21.40 S ATOM 5859 SG CYS G 159 80.938 52.485 179.366 1.00 21.77 S ATOM 6203 SG CYS G 203 82.998 57.642 176.241 1.00 19.87 S ATOM 6428 SG CYS G 230 79.235 49.329 155.062 1.00 31.37 S ATOM 6713 SG CYS G 265 79.286 45.578 160.449 1.00 35.22 S ATOM 6476 SG CYS G 237 73.964 49.082 158.326 1.00 18.03 S ATOM 6452 SG CYS G 233 76.068 43.634 155.347 1.00 36.75 S ATOM 4877 SG CYS G 36 71.566 59.377 182.749 1.00 29.66 S ATOM 4953 SG CYS G 47 73.332 62.642 183.013 1.00 50.07 S ATOM 4979 SG CYS G 50 67.591 64.581 183.079 1.00 38.67 S ATOM 5128 SG CYS G 69 66.998 60.946 183.016 1.00 44.68 S ATOM 17200 SG CYS B 129 94.079 92.874 150.497 1.00 30.04 S ATOM 16697 SG CYS B 64 99.391 96.540 151.965 1.00 33.49 S ATOM 16691 SG CYS B 63 93.938 98.721 153.950 1.00 36.23 S ATOM 17417 SG CYS B 158 96.028 92.883 156.287 1.00 42.48 S ATOM 18748 SG CYS I 102 94.800 87.072 162.464 1.00 15.72 S ATOM 18723 SG CYS I 99 100.168 85.666 158.686 1.00 46.21 S ATOM 18766 SG CYS I 105 98.840 82.439 164.172 1.00 39.22 S ATOM 18481 SG CYS I 70 94.878 81.737 159.068 1.00 18.70 S ATOM 18795 SG CYS I 109 99.840 76.893 170.485 1.00 20.26 S ATOM 18458 SG CYS I 66 97.732 76.187 164.399 1.00 17.39 S ATOM 18418 SG CYS I 60 101.786 71.817 166.593 1.00 17.60 S ATOM 18436 SG CYS I 63 95.605 72.420 169.208 1.00 25.20 S Time building chain proxies: 8.20, per 1000 atoms: 0.22 Number of scatterers: 37587 At special positions: 0 Unit cell: (157.94, 214.12, 245.92, 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 266 16.00 P 16 15.00 O 6583 8.00 N 6162 7.00 C 24527 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: 3.23 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " 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="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8602 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 0 sheets defined 51.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 4.834A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.625A 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: 4.356A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.726A 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: 5.193A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.065A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.667A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.042A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.608A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.224A 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: 4.592A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.991A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.639A 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: 4.656A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 5.024A 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: 4.553A 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 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.015A 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: 4.686A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 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: 4.495A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.202A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.358A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.541A 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 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.738A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1691 hydrogen bonds defined for protein. 5073 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: 6.25 Time building geometry restraints manager: 4.24 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: 15885 1.42 - 1.64: 22121 1.64 - 1.86: 408 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38506 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.47e+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=" C10 FMN F 502 " pdb=" N1 FMN F 502 " ideal model delta sigma weight residual 1.317 1.379 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.00e+00 ... (remaining 38501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 51743 3.51 - 7.03: 347 7.03 - 10.54: 51 10.54 - 14.05: 9 14.05 - 17.57: 2 Bond angle restraints: 52152 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 95.15 14.66 2.21e+00 2.05e-01 4.40e+01 angle pdb=" CA PRO J 90 " pdb=" N PRO J 90 " pdb=" CD PRO J 90 " ideal model delta sigma weight residual 112.00 104.13 7.87 1.40e+00 5.10e-01 3.16e+01 angle pdb=" CA GLN G 310 " pdb=" CB GLN G 310 " pdb=" CG GLN G 310 " ideal model delta sigma weight residual 114.10 124.42 -10.32 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CA LEU L 491 " pdb=" CB LEU L 491 " pdb=" CG LEU L 491 " ideal model delta sigma weight residual 116.30 133.87 -17.57 3.50e+00 8.16e-02 2.52e+01 angle pdb=" C MET E 26 " pdb=" N HIS E 27 " pdb=" CA HIS E 27 " ideal model delta sigma weight residual 121.94 112.35 9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 52147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 21467 25.98 - 51.96: 1149 51.96 - 77.93: 139 77.93 - 103.91: 17 103.91 - 129.89: 8 Dihedral angle restraints: 22780 sinusoidal: 9330 harmonic: 13450 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 180.00 133.17 46.83 0 5.00e+00 4.00e-02 8.77e+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 180.00 149.68 30.32 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA PRO N 387 " pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 22777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 5762 4.236 - 8.472: 0 8.472 - 12.708: 0 12.708 - 16.943: 0 16.943 - 21.179: 28 Chirality restraints: 5790 Sorted by residual: 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="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 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5787 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 B 302 " -0.037 2.00e-02 2.50e+03 7.68e-02 1.77e+02 pdb=" C1M UQ8 B 302 " -0.154 2.00e-02 2.50e+03 pdb=" C2 UQ8 B 302 " 0.051 2.00e-02 2.50e+03 pdb=" C3 UQ8 B 302 " -0.010 2.00e-02 2.50e+03 pdb=" C4 UQ8 B 302 " -0.004 2.00e-02 2.50e+03 pdb=" C5 UQ8 B 302 " 0.021 2.00e-02 2.50e+03 pdb=" C6 UQ8 B 302 " 0.023 2.00e-02 2.50e+03 pdb=" C7 UQ8 B 302 " 0.030 2.00e-02 2.50e+03 pdb=" O2 UQ8 B 302 " 0.173 2.00e-02 2.50e+03 pdb=" O3 UQ8 B 302 " -0.092 2.00e-02 2.50e+03 pdb=" O4 UQ8 B 302 " -0.038 2.00e-02 2.50e+03 pdb=" O5 UQ8 B 302 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO J 90 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C VAL N 63 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.026 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3089 2.74 - 3.28: 36984 3.28 - 3.82: 68347 3.82 - 4.36: 82899 4.36 - 4.90: 140324 Nonbonded interactions: 331643 Sorted by model distance: nonbonded pdb=" OE1 GLU H 36 " pdb=" OH TYR H 242 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.221 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.259 3.040 nonbonded pdb=" N THR N 64 " pdb=" O THR N 64 " model vdw 2.267 2.496 ... (remaining 331638 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: 0.420 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 35.930 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.009 0.821 38542 Z= 0.304 Angle : 0.811 17.568 52245 Z= 0.396 Chirality : 1.469 21.179 5790 Planarity : 0.006 0.139 6491 Dihedral : 15.447 129.891 14178 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 1.30 % Allowed : 16.05 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.11), residues: 4668 helix: 0.29 (0.09), residues: 2705 sheet: -0.76 (0.28), residues: 312 loop : -1.12 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 374 TYR 0.032 0.002 TYR L 428 PHE 0.043 0.002 PHE H 282 TRP 0.038 0.002 TRP H 54 HIS 0.012 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00551 (38506) covalent geometry : angle 0.79358 (52152) hydrogen bonds : bond 0.05729 ( 1691) hydrogen bonds : angle 4.55569 ( 5073) metal coordination : bond 0.23559 ( 36) metal coordination : angle 4.08066 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 434 time to evaluate : 1.404 Fit side-chains REVERT: G 877 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8560 (tp30) REVERT: G 904 ASP cc_start: 0.8298 (t0) cc_final: 0.8047 (t0) REVERT: C 193 GLU cc_start: 0.5130 (OUTLIER) cc_final: 0.3983 (mp0) REVERT: C 488 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5612 (tpt) REVERT: I 27 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8639 (tttp) REVERT: H 286 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8295 (ttt180) REVERT: L 72 ASP cc_start: 0.8111 (t0) cc_final: 0.7841 (t0) REVERT: L 258 MET cc_start: 0.8692 (mmm) cc_final: 0.8416 (tpp) REVERT: L 490 MET cc_start: 0.8391 (ttm) cc_final: 0.8000 (ttp) REVERT: M 466 PHE cc_start: 0.8186 (m-10) cc_final: 0.7192 (p90) REVERT: N 30 TRP cc_start: 0.8773 (t-100) cc_final: 0.7798 (t60) REVERT: K 97 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8232 (pp20) REVERT: J 115 ASN cc_start: 0.8798 (t0) cc_final: 0.8591 (t0) outliers start: 50 outliers final: 33 residues processed: 469 average time/residue: 0.7101 time to fit residues: 402.8244 Evaluate side-chains 459 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 424 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 351 CYS Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 489 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 0.5980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070619 restraints weight = 56677.002| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.56 r_work: 0.2889 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.258 38542 Z= 0.391 Angle : 2.503 64.843 52245 Z= 1.432 Chirality : 0.441 6.490 5790 Planarity : 0.004 0.083 6491 Dihedral : 10.431 126.977 5925 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.19 % Allowed : 14.38 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4668 helix: 1.10 (0.10), residues: 2694 sheet: -0.67 (0.29), residues: 307 loop : -0.83 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 374 TYR 0.022 0.001 TYR L 428 PHE 0.023 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.004 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.01139 (38506) covalent geometry : angle 2.17134 (52152) hydrogen bonds : bond 0.04759 ( 1691) hydrogen bonds : angle 4.10141 ( 5073) metal coordination : bond 0.03830 ( 36) metal coordination : angle 29.57781 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 441 time to evaluate : 1.224 Fit side-chains REVERT: F 243 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8559 (mmmt) REVERT: E 143 MET cc_start: 0.7940 (ttp) cc_final: 0.7578 (ttp) REVERT: G 85 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: G 877 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7628 (tp30) REVERT: G 904 ASP cc_start: 0.7737 (t0) cc_final: 0.7432 (t0) REVERT: I 27 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8456 (tttp) REVERT: I 53 ASP cc_start: 0.8651 (p0) cc_final: 0.8440 (p0) REVERT: I 153 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.6723 (mtt) REVERT: I 168 ASN cc_start: 0.8442 (m110) cc_final: 0.8071 (m-40) REVERT: H 122 MET cc_start: 0.8760 (mmm) cc_final: 0.8469 (mmp) REVERT: L 72 ASP cc_start: 0.7522 (t0) cc_final: 0.7157 (t0) REVERT: L 318 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7090 (t80) REVERT: M 291 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: M 303 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: M 374 MET cc_start: 0.8379 (mtm) cc_final: 0.8064 (ptp) REVERT: M 466 PHE cc_start: 0.7963 (m-10) cc_final: 0.7115 (p90) REVERT: N 30 TRP cc_start: 0.8452 (t-100) cc_final: 0.7473 (t60) REVERT: N 96 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8444 (mm-30) REVERT: N 150 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8301 (ttmt) REVERT: K 46 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7973 (t80) REVERT: J 115 ASN cc_start: 0.8683 (t0) cc_final: 0.8426 (t0) outliers start: 84 outliers final: 29 residues processed: 488 average time/residue: 0.7198 time to fit residues: 424.3285 Evaluate side-chains 464 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 150 LYS Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 116 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 377 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 310 GLN G 517 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN L 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067882 restraints weight = 56241.246| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.57 r_work: 0.2828 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38542 Z= 0.417 Angle : 2.505 60.906 52245 Z= 1.435 Chirality : 0.445 6.496 5790 Planarity : 0.004 0.066 6491 Dihedral : 10.102 126.679 5880 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 13.70 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4668 helix: 1.23 (0.10), residues: 2701 sheet: -0.67 (0.28), residues: 318 loop : -0.64 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 727 TYR 0.020 0.002 TYR L 428 PHE 0.027 0.002 PHE L 430 TRP 0.018 0.001 TRP L 143 HIS 0.006 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.01185 (38506) covalent geometry : angle 2.17990 (52152) hydrogen bonds : bond 0.05362 ( 1691) hydrogen bonds : angle 4.18828 ( 5073) metal coordination : bond 0.03951 ( 36) metal coordination : angle 29.33973 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 440 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 131 PHE cc_start: 0.8286 (t80) cc_final: 0.8075 (t80) REVERT: F 243 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8556 (mmmt) REVERT: F 249 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7869 (mm) REVERT: F 250 MET cc_start: 0.8042 (mtt) cc_final: 0.7426 (mpp) REVERT: E 143 MET cc_start: 0.8028 (ttp) cc_final: 0.7671 (ttp) REVERT: G 85 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: G 129 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7800 (ptm-80) REVERT: G 740 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6281 (tpt) REVERT: G 792 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8148 (mp0) REVERT: G 877 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7619 (tp30) REVERT: G 904 ASP cc_start: 0.7707 (t0) cc_final: 0.7358 (t0) REVERT: I 27 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8441 (tttp) REVERT: I 53 ASP cc_start: 0.8660 (p0) cc_final: 0.8447 (p0) REVERT: I 83 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (ptpt) REVERT: I 153 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.6777 (mtt) REVERT: H 63 ASP cc_start: 0.7815 (m-30) cc_final: 0.7611 (m-30) REVERT: H 122 MET cc_start: 0.8833 (mmm) cc_final: 0.8593 (mmp) REVERT: A 20 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8433 (mt) REVERT: L 72 ASP cc_start: 0.7530 (t0) cc_final: 0.7171 (t0) REVERT: L 139 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: L 258 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (mmt) REVERT: M 291 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8356 (mmm) REVERT: M 303 TRP cc_start: 0.9307 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: M 398 MET cc_start: 0.8457 (tpt) cc_final: 0.8222 (mmm) REVERT: N 30 TRP cc_start: 0.8477 (t-100) cc_final: 0.7504 (t60) REVERT: N 485 MET cc_start: 0.2884 (mmt) cc_final: 0.2425 (mmp) REVERT: K 46 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8148 (t80) REVERT: J 69 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8640 (t80) REVERT: J 162 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5087 (tp30) outliers start: 120 outliers final: 50 residues processed: 508 average time/residue: 0.7194 time to fit residues: 441.1557 Evaluate side-chains 479 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 415 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 316 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 360 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN G 310 GLN C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067455 restraints weight = 55949.266| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.42 r_work: 0.2832 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38542 Z= 0.411 Angle : 2.505 63.460 52245 Z= 1.434 Chirality : 0.444 6.474 5790 Planarity : 0.004 0.062 6491 Dihedral : 10.040 131.310 5880 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 2.92 % Allowed : 14.22 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4668 helix: 1.34 (0.10), residues: 2689 sheet: -0.61 (0.28), residues: 319 loop : -0.60 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 374 TYR 0.020 0.002 TYR L 428 PHE 0.026 0.002 PHE L 430 TRP 0.020 0.001 TRP L 143 HIS 0.005 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01174 (38506) covalent geometry : angle 2.17842 (52152) hydrogen bonds : bond 0.05298 ( 1691) hydrogen bonds : angle 4.17330 ( 5073) metal coordination : bond 0.03232 ( 36) metal coordination : angle 29.41552 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 435 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6760 (mmt) cc_final: 0.4904 (ptt) REVERT: F 249 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7651 (mm) REVERT: F 250 MET cc_start: 0.8106 (mtt) cc_final: 0.7418 (mpp) REVERT: E 143 MET cc_start: 0.8029 (ttp) cc_final: 0.7674 (ttp) REVERT: G 85 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: G 643 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8648 (p) REVERT: G 714 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7430 (ptp-110) REVERT: G 740 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6345 (tpt) REVERT: G 792 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8130 (mp0) REVERT: G 877 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7591 (tp30) REVERT: G 904 ASP cc_start: 0.7772 (t0) cc_final: 0.7383 (t0) REVERT: C 488 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6015 (mmp) REVERT: I 27 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8514 (tttp) REVERT: I 53 ASP cc_start: 0.8644 (p0) cc_final: 0.8444 (p0) REVERT: I 83 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8664 (ptpt) REVERT: I 153 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: H 32 MET cc_start: 0.5499 (tpp) cc_final: 0.5115 (mpm) REVERT: H 63 ASP cc_start: 0.7770 (m-30) cc_final: 0.7457 (m-30) REVERT: A 20 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (mt) REVERT: L 72 ASP cc_start: 0.7592 (t0) cc_final: 0.7232 (t0) REVERT: L 139 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8447 (ttp) REVERT: M 291 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: M 303 TRP cc_start: 0.9310 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: M 398 MET cc_start: 0.8409 (tpt) cc_final: 0.8179 (mmm) REVERT: M 466 PHE cc_start: 0.8157 (m-10) cc_final: 0.7274 (p90) REVERT: N 30 TRP cc_start: 0.8460 (t-100) cc_final: 0.7492 (t60) REVERT: N 485 MET cc_start: 0.3110 (mmt) cc_final: 0.2858 (mmp) REVERT: K 46 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8156 (t80) REVERT: J 69 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8613 (t80) REVERT: J 162 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.5037 (tp30) outliers start: 112 outliers final: 43 residues processed: 497 average time/residue: 0.7191 time to fit residues: 429.9805 Evaluate side-chains 471 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 413 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 444 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 253 optimal weight: 0.0000 chunk 197 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 416 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 106 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN L 58 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.067408 restraints weight = 55361.773| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.42 r_work: 0.2829 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38542 Z= 0.406 Angle : 2.505 63.283 52245 Z= 1.434 Chirality : 0.443 6.445 5790 Planarity : 0.004 0.060 6491 Dihedral : 9.962 133.648 5877 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 3.23 % Allowed : 14.33 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 4668 helix: 1.40 (0.10), residues: 2693 sheet: -0.62 (0.28), residues: 319 loop : -0.53 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 727 TYR 0.020 0.002 TYR L 428 PHE 0.029 0.002 PHE L 430 TRP 0.020 0.001 TRP L 143 HIS 0.005 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01164 (38506) covalent geometry : angle 2.17725 (52152) hydrogen bonds : bond 0.05214 ( 1691) hydrogen bonds : angle 4.16434 ( 5073) metal coordination : bond 0.03053 ( 36) metal coordination : angle 29.43687 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 427 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6879 (mmt) cc_final: 0.4972 (ptt) REVERT: F 249 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7565 (mm) REVERT: F 250 MET cc_start: 0.7977 (mtt) cc_final: 0.7291 (mpp) REVERT: F 386 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7965 (tm-30) REVERT: E 143 MET cc_start: 0.8011 (ttp) cc_final: 0.7667 (ttp) REVERT: G 85 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: G 129 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7907 (ptm-80) REVERT: G 643 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (p) REVERT: G 714 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7365 (ptp-110) REVERT: G 740 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6375 (tpt) REVERT: G 792 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8103 (mp0) REVERT: G 877 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7647 (tp30) REVERT: G 904 ASP cc_start: 0.7805 (t0) cc_final: 0.7401 (t0) REVERT: I 1 MET cc_start: 0.6289 (pmm) cc_final: 0.6055 (pmm) REVERT: I 27 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8485 (tttp) REVERT: I 83 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8593 (ptpt) REVERT: I 153 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.6776 (mtt) REVERT: I 171 LYS cc_start: 0.8310 (mttm) cc_final: 0.8053 (mmmt) REVERT: H 32 MET cc_start: 0.5515 (tpp) cc_final: 0.4974 (ttm) REVERT: H 63 ASP cc_start: 0.7763 (m-30) cc_final: 0.7471 (m-30) REVERT: H 157 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 20 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8423 (mt) REVERT: L 72 ASP cc_start: 0.7575 (t0) cc_final: 0.7221 (t0) REVERT: L 139 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8402 (ttp) REVERT: M 291 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8324 (mmm) REVERT: M 303 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: M 466 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7277 (p90) REVERT: N 30 TRP cc_start: 0.8447 (t-100) cc_final: 0.7475 (t60) REVERT: N 197 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6447 (mmm) REVERT: N 485 MET cc_start: 0.3261 (mmt) cc_final: 0.2734 (mmp) REVERT: K 46 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8172 (t80) REVERT: J 69 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8576 (t80) outliers start: 124 outliers final: 66 residues processed: 497 average time/residue: 0.7123 time to fit residues: 427.9840 Evaluate side-chains 493 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 411 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 553 GLU Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 404 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 3 optimal weight: 0.0470 chunk 352 optimal weight: 8.9990 chunk 457 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 355 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 106 GLN G 901 HIS C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN L 58 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.067058 restraints weight = 55210.508| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.52 r_work: 0.2809 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38542 Z= 0.419 Angle : 2.510 63.949 52245 Z= 1.436 Chirality : 0.444 6.464 5790 Planarity : 0.004 0.059 6491 Dihedral : 10.003 134.973 5877 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 3.36 % Allowed : 14.61 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4668 helix: 1.38 (0.10), residues: 2692 sheet: -0.62 (0.28), residues: 318 loop : -0.53 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 727 TYR 0.020 0.002 TYR L 428 PHE 0.026 0.002 PHE L 430 TRP 0.021 0.001 TRP L 143 HIS 0.005 0.001 HIS N 124 Details of bonding type rmsd covalent geometry : bond 0.01189 (38506) covalent geometry : angle 2.18339 (52152) hydrogen bonds : bond 0.05416 ( 1691) hydrogen bonds : angle 4.21408 ( 5073) metal coordination : bond 0.03280 ( 36) metal coordination : angle 29.43210 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 419 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6819 (mmt) cc_final: 0.5003 (ptt) REVERT: F 249 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7562 (mm) REVERT: F 250 MET cc_start: 0.8047 (mtt) cc_final: 0.7394 (mpp) REVERT: F 291 GLN cc_start: 0.7760 (tt0) cc_final: 0.7503 (tt0) REVERT: F 386 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 143 MET cc_start: 0.8050 (ttp) cc_final: 0.7715 (ttp) REVERT: G 85 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: G 129 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7951 (ptm-80) REVERT: G 643 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8665 (p) REVERT: G 714 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7396 (ptp-110) REVERT: G 740 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6386 (tpt) REVERT: G 792 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8107 (mp0) REVERT: G 877 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7650 (tp30) REVERT: G 904 ASP cc_start: 0.7845 (t0) cc_final: 0.7424 (t0) REVERT: I 27 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8489 (tttp) REVERT: I 83 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8606 (ptpt) REVERT: I 153 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.6787 (mtt) REVERT: I 171 LYS cc_start: 0.8322 (mttm) cc_final: 0.8073 (mmmt) REVERT: H 32 MET cc_start: 0.5526 (tpp) cc_final: 0.4981 (ttm) REVERT: H 63 ASP cc_start: 0.7832 (m-30) cc_final: 0.7467 (m-30) REVERT: H 64 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6642 (mmm) REVERT: H 67 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8172 (mmt) REVERT: A 20 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 64 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8503 (mm) REVERT: L 72 ASP cc_start: 0.7604 (t0) cc_final: 0.7248 (t0) REVERT: L 139 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: M 291 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (mmm) REVERT: M 303 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8290 (m-10) REVERT: M 466 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7306 (p90) REVERT: N 30 TRP cc_start: 0.8468 (t-100) cc_final: 0.7476 (t60) REVERT: N 197 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6424 (mmm) REVERT: N 485 MET cc_start: 0.3321 (mmt) cc_final: 0.2794 (mmp) REVERT: K 46 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8168 (t80) REVERT: J 69 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8585 (t80) outliers start: 129 outliers final: 72 residues processed: 495 average time/residue: 0.7237 time to fit residues: 433.7721 Evaluate side-chains 498 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 407 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 553 GLU Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 392 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 443 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 390 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 422 optimal weight: 4.9990 chunk 379 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 106 GLN C 162 GLN C 359 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067885 restraints weight = 55491.430| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.42 r_work: 0.2839 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38542 Z= 0.396 Angle : 2.503 63.650 52245 Z= 1.433 Chirality : 0.442 6.421 5790 Planarity : 0.004 0.059 6491 Dihedral : 9.813 137.284 5877 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.81 % Favored : 97.17 % Rotamer: Outliers : 2.94 % Allowed : 15.19 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4668 helix: 1.51 (0.10), residues: 2691 sheet: -0.58 (0.28), residues: 316 loop : -0.48 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 727 TYR 0.022 0.002 TYR M 435 PHE 0.027 0.001 PHE L 430 TRP 0.019 0.001 TRP L 143 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.01147 (38506) covalent geometry : angle 2.17544 (52152) hydrogen bonds : bond 0.04998 ( 1691) hydrogen bonds : angle 4.13400 ( 5073) metal coordination : bond 0.02773 ( 36) metal coordination : angle 29.44267 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 427 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6850 (mmt) cc_final: 0.5043 (ptt) REVERT: F 249 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7525 (mm) REVERT: F 250 MET cc_start: 0.8067 (mtt) cc_final: 0.7360 (mpp) REVERT: F 386 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 143 MET cc_start: 0.8020 (ttp) cc_final: 0.7691 (ttp) REVERT: G 85 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: G 129 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7902 (ptm-80) REVERT: G 643 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8635 (p) REVERT: G 714 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7338 (ptp-110) REVERT: G 740 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6450 (tpt) REVERT: G 792 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8100 (mp0) REVERT: G 877 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7618 (tp30) REVERT: G 904 ASP cc_start: 0.7860 (t0) cc_final: 0.7434 (t0) REVERT: C 488 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6074 (mmp) REVERT: I 27 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8487 (tttp) REVERT: I 83 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8596 (ptpt) REVERT: I 153 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.6774 (mtt) REVERT: I 171 LYS cc_start: 0.8328 (mttm) cc_final: 0.8073 (mmmt) REVERT: H 32 MET cc_start: 0.5489 (tpp) cc_final: 0.4997 (ttm) REVERT: H 63 ASP cc_start: 0.7817 (m-30) cc_final: 0.7505 (m-30) REVERT: H 157 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 20 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 64 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 110 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7929 (mt) REVERT: L 72 ASP cc_start: 0.7592 (t0) cc_final: 0.7246 (t0) REVERT: L 139 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8404 (ttp) REVERT: M 291 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: M 303 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: N 30 TRP cc_start: 0.8459 (t-100) cc_final: 0.7467 (t60) REVERT: N 485 MET cc_start: 0.3226 (mmt) cc_final: 0.2794 (mmp) REVERT: K 46 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8225 (t80) outliers start: 113 outliers final: 64 residues processed: 498 average time/residue: 0.7117 time to fit residues: 428.9374 Evaluate side-chains 495 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 415 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 169 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 303 optimal weight: 0.0270 chunk 246 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 428 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN E 46 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN L 58 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.069182 restraints weight = 55292.193| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.41 r_work: 0.2868 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38542 Z= 0.386 Angle : 2.502 62.500 52245 Z= 1.432 Chirality : 0.441 6.392 5790 Planarity : 0.004 0.059 6491 Dihedral : 9.571 138.230 5877 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.50 % Allowed : 15.92 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 4668 helix: 1.66 (0.10), residues: 2681 sheet: -0.49 (0.29), residues: 314 loop : -0.46 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 727 TYR 0.024 0.001 TYR M 435 PHE 0.025 0.001 PHE L 430 TRP 0.019 0.001 TRP F 262 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.01130 (38506) covalent geometry : angle 2.17170 (52152) hydrogen bonds : bond 0.04611 ( 1691) hydrogen bonds : angle 4.04417 ( 5073) metal coordination : bond 0.02419 ( 36) metal coordination : angle 29.52856 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 440 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6771 (mmt) cc_final: 0.5097 (ptt) REVERT: F 386 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7875 (tm-30) REVERT: E 143 MET cc_start: 0.8031 (ttp) cc_final: 0.7699 (ttp) REVERT: G 85 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: G 129 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7815 (ptm-80) REVERT: G 643 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8617 (p) REVERT: G 714 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7326 (ptp-110) REVERT: G 740 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6462 (tpt) REVERT: G 792 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8104 (mp0) REVERT: G 859 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7957 (mtp85) REVERT: G 877 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7629 (tp30) REVERT: G 904 ASP cc_start: 0.7880 (t0) cc_final: 0.7440 (t0) REVERT: C 488 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5842 (tpt) REVERT: I 83 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8603 (ptpt) REVERT: I 153 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.6767 (mtt) REVERT: H 32 MET cc_start: 0.5378 (tpp) cc_final: 0.4991 (ttm) REVERT: H 63 ASP cc_start: 0.7848 (m-30) cc_final: 0.7534 (m-30) REVERT: A 20 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 64 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8456 (mm) REVERT: L 72 ASP cc_start: 0.7645 (t0) cc_final: 0.7308 (t0) REVERT: L 139 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8395 (ttp) REVERT: M 291 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: M 303 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: N 30 TRP cc_start: 0.8425 (t-100) cc_final: 0.7449 (t60) REVERT: N 485 MET cc_start: 0.3172 (mmt) cc_final: 0.2577 (mmp) REVERT: K 46 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8194 (t80) outliers start: 96 outliers final: 52 residues processed: 501 average time/residue: 0.7217 time to fit residues: 437.3218 Evaluate side-chains 483 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 417 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 306 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 458 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 459 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN E 27 HIS E 46 GLN E 106 GLN C 78 HIS B 196 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068049 restraints weight = 55605.799| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.42 r_work: 0.2842 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38542 Z= 0.398 Angle : 2.507 62.281 52245 Z= 1.434 Chirality : 0.442 6.431 5790 Planarity : 0.004 0.061 6491 Dihedral : 9.618 139.271 5877 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 2.32 % Allowed : 16.05 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4668 helix: 1.62 (0.10), residues: 2685 sheet: -0.50 (0.29), residues: 316 loop : -0.45 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 727 TYR 0.021 0.002 TYR L 428 PHE 0.027 0.001 PHE L 430 TRP 0.025 0.001 TRP F 262 HIS 0.006 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.01152 (38506) covalent geometry : angle 2.17949 (52152) hydrogen bonds : bond 0.04961 ( 1691) hydrogen bonds : angle 4.11009 ( 5073) metal coordination : bond 0.02851 ( 36) metal coordination : angle 29.44837 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 423 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 386 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 143 MET cc_start: 0.8115 (ttp) cc_final: 0.7787 (ttp) REVERT: G 85 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: G 129 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7936 (ptm-80) REVERT: G 643 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (p) REVERT: G 714 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7343 (ptp-110) REVERT: G 740 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6336 (tpt) REVERT: G 792 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8106 (mp0) REVERT: G 859 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7945 (mtp85) REVERT: G 877 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7930 (tp30) REVERT: G 904 ASP cc_start: 0.7915 (t0) cc_final: 0.7473 (t0) REVERT: C 488 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6138 (tpt) REVERT: I 27 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8541 (tttp) REVERT: I 83 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8590 (ptpt) REVERT: I 153 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.6877 (mtt) REVERT: H 32 MET cc_start: 0.5378 (tpp) cc_final: 0.4932 (ttm) REVERT: H 63 ASP cc_start: 0.7827 (m-30) cc_final: 0.7489 (m-30) REVERT: A 20 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 64 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (mm) REVERT: L 72 ASP cc_start: 0.7621 (t0) cc_final: 0.7323 (t0) REVERT: L 139 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8377 (ttp) REVERT: M 303 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: N 30 TRP cc_start: 0.8439 (t-100) cc_final: 0.7460 (t60) REVERT: N 485 MET cc_start: 0.3020 (mmt) cc_final: 0.2475 (mmp) REVERT: K 46 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8213 (t80) REVERT: K 97 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7952 (mt-10) outliers start: 89 outliers final: 57 residues processed: 477 average time/residue: 0.7126 time to fit residues: 410.7613 Evaluate side-chains 488 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 418 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 481 GLN Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 271 optimal weight: 9.9990 chunk 411 optimal weight: 0.0070 chunk 403 optimal weight: 4.9990 chunk 441 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 447 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN B 196 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN L 58 GLN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068366 restraints weight = 55249.910| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.42 r_work: 0.2849 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38542 Z= 0.395 Angle : 2.508 62.420 52245 Z= 1.434 Chirality : 0.442 6.424 5790 Planarity : 0.004 0.066 6491 Dihedral : 9.579 140.344 5877 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 2.11 % Allowed : 16.59 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.12), residues: 4668 helix: 1.64 (0.10), residues: 2683 sheet: -0.52 (0.29), residues: 316 loop : -0.45 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 727 TYR 0.021 0.002 TYR L 428 PHE 0.027 0.001 PHE L 430 TRP 0.024 0.001 TRP F 262 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.01145 (38506) covalent geometry : angle 2.18050 (52152) hydrogen bonds : bond 0.04887 ( 1691) hydrogen bonds : angle 4.10902 ( 5073) metal coordination : bond 0.02735 ( 36) metal coordination : angle 29.47107 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 425 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 161 MET cc_start: 0.6857 (mmt) cc_final: 0.4606 (ptt) REVERT: F 386 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 143 MET cc_start: 0.8083 (ttp) cc_final: 0.7760 (ttp) REVERT: G 56 GLN cc_start: 0.7964 (mp10) cc_final: 0.7579 (mp10) REVERT: G 85 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: G 129 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7921 (ptm-80) REVERT: G 643 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8627 (p) REVERT: G 714 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7345 (ptp-110) REVERT: G 740 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6354 (tpt) REVERT: G 792 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8107 (mp0) REVERT: G 859 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7948 (mtp85) REVERT: G 877 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7924 (tp30) REVERT: G 904 ASP cc_start: 0.7916 (t0) cc_final: 0.7477 (t0) REVERT: C 488 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6217 (tpt) REVERT: I 27 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8502 (tttp) REVERT: I 83 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8592 (ptpt) REVERT: I 153 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: H 32 MET cc_start: 0.5366 (tpp) cc_final: 0.4932 (ttm) REVERT: H 63 ASP cc_start: 0.7849 (m-30) cc_final: 0.7522 (m-30) REVERT: A 20 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 64 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8460 (mm) REVERT: L 72 ASP cc_start: 0.7639 (t0) cc_final: 0.7360 (t0) REVERT: L 139 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8399 (ttp) REVERT: M 303 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: N 30 TRP cc_start: 0.8439 (t-100) cc_final: 0.7427 (t60) REVERT: N 31 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7871 (ttp-110) REVERT: N 485 MET cc_start: 0.3187 (mmt) cc_final: 0.2617 (mmp) REVERT: K 46 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8211 (t80) REVERT: K 97 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7916 (mt-10) outliers start: 81 outliers final: 56 residues processed: 472 average time/residue: 0.7412 time to fit residues: 422.1944 Evaluate side-chains 490 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 481 GLN Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 282 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 393 optimal weight: 0.4980 chunk 237 optimal weight: 9.9990 chunk 418 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 429 optimal weight: 0.7980 chunk 346 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 106 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN N 37 ASN N 57 GLN N 317 GLN K 82 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070927 restraints weight = 55727.670| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.42 r_work: 0.2906 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38542 Z= 0.382 Angle : 2.504 60.259 52245 Z= 1.431 Chirality : 0.440 6.378 5790 Planarity : 0.004 0.067 6491 Dihedral : 9.225 140.474 5877 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 17.24 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4668 helix: 1.81 (0.10), residues: 2682 sheet: -0.36 (0.29), residues: 315 loop : -0.40 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 727 TYR 0.028 0.001 TYR M 435 PHE 0.023 0.001 PHE L 430 TRP 0.023 0.001 TRP F 262 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.01123 (38506) covalent geometry : angle 2.17250 (52152) hydrogen bonds : bond 0.04231 ( 1691) hydrogen bonds : angle 3.96673 ( 5073) metal coordination : bond 0.01988 ( 36) metal coordination : angle 29.57235 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14496.18 seconds wall clock time: 246 minutes 46.67 seconds (14806.67 seconds total)