Starting phenix.real_space_refine on Sat Mar 7 03:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z84_14542/03_2026/7z84_14542.map" } resolution = 2.87 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= 0.018 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 13 5.49 5 S 267 5.16 5 C 24594 2.51 5 N 6239 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s 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: 37772 Number of models: 1 Model: "" Number of chains: 23 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: 4738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4738 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} 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: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2544 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 307} Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4629 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 224 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 70.269 60.480 191.525 1.00 12.70 S ATOM 2741 SG CYS F 357 73.673 60.035 196.087 1.00 22.22 S ATOM 3062 SG CYS F 398 67.840 56.764 196.394 1.00 21.57 S ATOM 2697 SG CYS F 351 72.337 54.157 192.920 1.00 14.65 S ATOM 4054 SG CYS E 92 80.559 52.057 212.775 1.00 36.01 S ATOM 4088 SG CYS E 97 80.635 52.886 216.206 1.00 34.35 S ATOM 4366 SG CYS E 133 75.310 51.456 212.367 1.00 47.06 S ATOM 4392 SG CYS E 137 74.503 52.311 215.614 1.00 40.65 S ATOM 5476 SG CYS G 114 81.024 66.621 174.325 1.00 7.04 S ATOM 5416 SG CYS G 105 86.283 70.282 175.941 1.00 7.35 S ATOM 5436 SG CYS G 108 86.951 64.315 173.544 1.00 1.74 S ATOM 5830 SG CYS G 156 75.140 58.831 179.129 1.00 6.41 S ATOM 5811 SG CYS G 153 80.906 57.673 182.204 1.00 3.89 S ATOM 5859 SG CYS G 159 78.175 53.080 178.565 1.00 5.98 S ATOM 6203 SG CYS G 203 80.322 58.302 175.556 1.00 5.88 S ATOM 6428 SG CYS G 230 77.315 49.982 154.306 1.00 15.43 S ATOM 6713 SG CYS G 265 77.106 46.208 159.640 1.00 9.98 S ATOM 6476 SG CYS G 237 71.846 49.626 157.339 1.00 4.70 S ATOM 6452 SG CYS G 233 74.080 44.297 154.329 1.00 18.49 S ATOM 4877 SG CYS G 36 68.783 59.853 181.861 1.00 4.16 S ATOM 4953 SG CYS G 47 70.341 63.183 182.112 1.00 3.85 S ATOM 4979 SG CYS G 50 64.517 64.874 181.919 1.00 11.43 S ATOM 5128 SG CYS G 69 63.989 61.326 181.695 1.00 9.98 S ATOM 17321 SG CYS B 129 91.859 93.860 150.601 1.00 8.44 S ATOM 16818 SG CYS B 64 97.099 97.582 152.343 1.00 15.77 S ATOM 16812 SG CYS B 63 91.569 99.706 154.130 1.00 7.15 S ATOM 17538 SG CYS B 158 93.531 93.758 156.386 1.00 11.15 S ATOM 18869 SG CYS I 102 92.212 87.977 162.405 1.00 2.12 S ATOM 18844 SG CYS I 99 97.671 86.527 158.865 1.00 6.35 S ATOM 18887 SG CYS I 105 96.165 83.229 164.254 1.00 9.95 S ATOM 18602 SG CYS I 70 92.343 82.644 159.000 1.00 7.39 S ATOM 18916 SG CYS I 109 97.040 77.666 170.519 1.00 3.35 S ATOM 18579 SG CYS I 66 95.124 77.030 164.366 1.00 13.84 S ATOM 18539 SG CYS I 60 99.102 72.628 166.711 1.00 7.86 S ATOM 18557 SG CYS I 63 92.828 73.186 169.088 1.00 6.93 S Time building chain proxies: 8.02, per 1000 atoms: 0.21 Number of scatterers: 37772 At special positions: 0 Unit cell: (157.94, 215.18, 243.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 13 15.00 O 6626 8.00 N 6239 7.00 C 24594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="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="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 51.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 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: 4.868A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.422A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.829A 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: 5.075A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.384A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.958A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.810A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 9.065A pdb=" N THR C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N LYS C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) 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: 4.040A 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: 4.730A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.588A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.463A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.961A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.673A 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: 4.527A 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: 4.155A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.883A 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 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.102A 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: 4.700A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.327A 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: 4.507A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.281A 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: 4.191A 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: 4.472A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.412A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.062A 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 1708 hydrogen bonds defined for protein. 5124 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: 6.75 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 16045 1.42 - 1.64: 22166 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38712 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 2.37e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.37e+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 1.18e+01 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" O13 3PE J 202 " pdb=" P 3PE J 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 ... (remaining 38707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 52089 3.39 - 6.79: 325 6.79 - 10.18: 59 10.18 - 13.58: 10 13.58 - 16.97: 3 Bond angle restraints: 52486 Sorted by residual: angle pdb=" C TYR C 268 " pdb=" N ILE C 269 " pdb=" CA ILE C 269 " ideal model delta sigma weight residual 120.24 124.68 -4.44 6.30e-01 2.52e+00 4.97e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.03 12.78 2.21e+00 2.05e-01 3.34e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 129.67 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" CB LYS L 515 " pdb=" CG LYS L 515 " pdb=" CD LYS L 515 " ideal model delta sigma weight residual 111.30 124.17 -12.87 2.30e+00 1.89e-01 3.13e+01 angle pdb=" CB MET N 255 " pdb=" CG MET N 255 " pdb=" SD MET N 255 " ideal model delta sigma weight residual 112.70 129.36 -16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 52481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.32: 21418 27.32 - 54.64: 1307 54.64 - 81.97: 132 81.97 - 109.29: 19 109.29 - 136.61: 3 Dihedral angle restraints: 22879 sinusoidal: 9306 harmonic: 13573 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.31 44.69 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.05 34.95 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA THR L 257 " pdb=" C THR L 257 " pdb=" N MET L 258 " pdb=" CA MET L 258 " ideal model delta harmonic sigma weight residual -180.00 -145.75 -34.25 0 5.00e+00 4.00e-02 4.69e+01 ... (remaining 22876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 5813 4.237 - 8.473: 0 8.473 - 12.710: 0 12.710 - 16.947: 0 16.947 - 21.183: 28 Chirality restraints: 5841 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5838 not shown) Planarity restraints: 6554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C VAL N 63 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.028 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 201 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 93 " 0.021 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP J 93 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP J 93 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J 93 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 93 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 93 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 93 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 93 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 6551 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5009 2.76 - 3.29: 36241 3.29 - 3.83: 69587 3.83 - 4.36: 83838 4.36 - 4.90: 141055 Nonbonded interactions: 335730 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.221 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.244 3.040 nonbonded pdb=" O TRP G 668 " pdb=" OG1 THR G 669 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.256 3.040 ... (remaining 335725 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 38748 Z= 0.215 Angle : 0.785 16.974 52579 Z= 0.389 Chirality : 1.464 21.183 5841 Planarity : 0.006 0.104 6554 Dihedral : 16.699 136.612 14197 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 20.05 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: -0.27 (0.11), residues: 4711 helix: 0.35 (0.09), residues: 2673 sheet: -0.40 (0.27), residues: 323 loop : -0.80 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 198 TYR 0.032 0.002 TYR M 435 PHE 0.042 0.002 PHE L 341 TRP 0.060 0.002 TRP J 93 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00452 (38712) covalent geometry : angle 0.76960 (52486) hydrogen bonds : bond 0.05372 ( 1708) hydrogen bonds : angle 4.65303 ( 5124) metal coordination : bond 0.05417 ( 36) metal coordination : angle 3.77301 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 489 time to evaluate : 1.401 Fit side-chains REVERT: F 80 GLU cc_start: 0.7466 (mp0) cc_final: 0.7064 (pm20) REVERT: F 126 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8036 (p90) REVERT: G 62 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7034 (tpt170) REVERT: L 198 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7958 (mtt180) REVERT: L 258 MET cc_start: 0.8059 (mmm) cc_final: 0.6660 (tmm) REVERT: M 441 HIS cc_start: 0.8170 (m170) cc_final: 0.7792 (m170) REVERT: N 106 TYR cc_start: 0.8626 (m-80) cc_final: 0.8265 (m-80) REVERT: N 135 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8691 (tt) REVERT: N 388 MET cc_start: 0.7978 (mtm) cc_final: 0.7638 (mtp) outliers start: 64 outliers final: 41 residues processed: 547 average time/residue: 0.6770 time to fit residues: 450.0337 Evaluate side-chains 492 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 449 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 497 SER Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 608 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 455 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 400 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN G 765 GLN G 768 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 45 ASN L 163 ASN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073274 restraints weight = 51413.058| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.26 r_work: 0.2907 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.255 38748 Z= 0.390 Angle : 2.479 50.821 52579 Z= 1.425 Chirality : 0.444 6.480 5841 Planarity : 0.004 0.071 6554 Dihedral : 9.335 137.476 5826 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 2.93 % Allowed : 18.01 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.54 (0.12), residues: 4711 helix: 1.09 (0.10), residues: 2677 sheet: -0.13 (0.28), residues: 302 loop : -0.61 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 198 TYR 0.022 0.001 TYR L 428 PHE 0.030 0.001 PHE L 341 TRP 0.028 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01131 (38712) covalent geometry : angle 2.16096 (52486) hydrogen bonds : bond 0.04871 ( 1708) hydrogen bonds : angle 4.16210 ( 5124) metal coordination : bond 0.04978 ( 36) metal coordination : angle 28.95376 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 458 time to evaluate : 1.446 Fit side-chains REVERT: F 126 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8566 (p90) REVERT: F 307 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8571 (mp) REVERT: G 459 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9056 (tp) REVERT: G 541 MET cc_start: 0.8876 (mmt) cc_final: 0.8448 (mmt) REVERT: G 670 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7720 (tm130) REVERT: B 126 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8526 (ttt) REVERT: B 170 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8376 (mtp) REVERT: A 108 PHE cc_start: 0.8640 (t80) cc_final: 0.8439 (t80) REVERT: L 168 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7175 (mtm) REVERT: L 353 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6606 (mp) REVERT: M 384 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8433 (tt) REVERT: N 379 MET cc_start: 0.9074 (mmt) cc_final: 0.8592 (mmt) REVERT: N 388 MET cc_start: 0.7919 (mtm) cc_final: 0.7409 (mtp) REVERT: N 482 MET cc_start: 0.8250 (tpp) cc_final: 0.7943 (mmm) REVERT: J 122 THR cc_start: 0.9103 (m) cc_final: 0.8597 (p) outliers start: 114 outliers final: 39 residues processed: 531 average time/residue: 0.6906 time to fit residues: 444.9209 Evaluate side-chains 489 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 442 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 249 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 462 optimal weight: 0.0370 chunk 345 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 310 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 424 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 458 optimal weight: 9.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 98 HIS G 299 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN H 152 GLN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 124 HIS J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075650 restraints weight = 51472.747| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.28 r_work: 0.2942 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38748 Z= 0.381 Angle : 2.475 50.797 52579 Z= 1.423 Chirality : 0.440 6.420 5841 Planarity : 0.004 0.073 6554 Dihedral : 8.840 136.260 5791 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.19 % Allowed : 17.81 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.99 (0.12), residues: 4711 helix: 1.50 (0.10), residues: 2672 sheet: -0.09 (0.28), residues: 319 loop : -0.46 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 198 TYR 0.025 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.025 0.001 TRP J 93 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01118 (38712) covalent geometry : angle 2.15261 (52486) hydrogen bonds : bond 0.04322 ( 1708) hydrogen bonds : angle 3.96474 ( 5124) metal coordination : bond 0.03285 ( 36) metal coordination : angle 29.12780 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 487 time to evaluate : 1.481 Fit side-chains REVERT: F 95 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8402 (tp30) REVERT: F 373 ARG cc_start: 0.8007 (mpp80) cc_final: 0.7374 (mtm-85) REVERT: F 388 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8169 (m) REVERT: E 103 GLN cc_start: 0.8714 (mp10) cc_final: 0.8410 (mp10) REVERT: G 98 MET cc_start: 0.9075 (mmp) cc_final: 0.8592 (mmp) REVERT: G 459 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9030 (tp) REVERT: G 541 MET cc_start: 0.8889 (mmt) cc_final: 0.8494 (mmt) REVERT: G 670 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7382 (tm130) REVERT: G 833 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: G 834 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: C 190 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: B 126 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8525 (ttt) REVERT: H 140 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7268 (pptt) REVERT: A 81 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: A 108 PHE cc_start: 0.8677 (t80) cc_final: 0.8456 (t80) REVERT: L 40 LEU cc_start: 0.8769 (mp) cc_final: 0.8523 (mt) REVERT: L 199 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: L 353 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6593 (mp) REVERT: L 546 ASP cc_start: 0.8059 (t70) cc_final: 0.7668 (t0) REVERT: M 384 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8398 (tt) REVERT: N 379 MET cc_start: 0.9121 (mmt) cc_final: 0.8659 (mmt) REVERT: N 388 MET cc_start: 0.7792 (mtm) cc_final: 0.7248 (mtp) REVERT: N 482 MET cc_start: 0.8180 (tpp) cc_final: 0.7939 (mmm) REVERT: J 122 THR cc_start: 0.9170 (m) cc_final: 0.8788 (p) outliers start: 124 outliers final: 39 residues processed: 571 average time/residue: 0.7018 time to fit residues: 484.0841 Evaluate side-chains 508 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 457 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 142 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 428 optimal weight: 10.0000 chunk 101 optimal weight: 0.0060 chunk 387 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 450 optimal weight: 0.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 386 GLN E 98 HIS G 839 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 190 GLN H 45 ASN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071427 restraints weight = 50899.398| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.25 r_work: 0.2868 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38748 Z= 0.407 Angle : 2.484 50.682 52579 Z= 1.428 Chirality : 0.444 6.554 5841 Planarity : 0.004 0.070 6554 Dihedral : 8.783 136.524 5774 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.17 % Favored : 97.81 % Rotamer: Outliers : 3.50 % Allowed : 17.78 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 4711 helix: 1.47 (0.10), residues: 2691 sheet: 0.05 (0.30), residues: 294 loop : -0.42 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 198 TYR 0.020 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.022 0.001 TRP J 93 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01161 (38712) covalent geometry : angle 2.16617 (52486) hydrogen bonds : bond 0.05170 ( 1708) hydrogen bonds : angle 4.11765 ( 5124) metal coordination : bond 0.04602 ( 36) metal coordination : angle 28.98734 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 457 time to evaluate : 1.493 Fit side-chains REVERT: F 307 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (mp) REVERT: F 420 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7957 (mp0) REVERT: G 98 MET cc_start: 0.9117 (mmp) cc_final: 0.8705 (mmp) REVERT: G 541 MET cc_start: 0.8891 (mmt) cc_final: 0.8449 (mmt) REVERT: G 670 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7722 (tm130) REVERT: G 834 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: C 190 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8101 (tp40) REVERT: C 276 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 378 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7963 (ttp-110) REVERT: B 166 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8474 (mtt) REVERT: H 140 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7509 (pptt) REVERT: A 29 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8335 (mm) REVERT: L 40 LEU cc_start: 0.8878 (mp) cc_final: 0.8548 (mt) REVERT: L 139 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: L 199 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: L 241 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6691 (t0) REVERT: L 258 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.6829 (tmm) REVERT: L 353 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6511 (mp) REVERT: L 546 ASP cc_start: 0.8084 (t70) cc_final: 0.7758 (t0) REVERT: M 291 MET cc_start: 0.8941 (mtp) cc_final: 0.8662 (mtp) REVERT: M 303 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: M 345 MET cc_start: 0.8150 (ptp) cc_final: 0.7908 (ptp) REVERT: M 384 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8458 (tt) REVERT: N 379 MET cc_start: 0.9122 (mmt) cc_final: 0.8695 (mmt) REVERT: N 482 MET cc_start: 0.8263 (tpp) cc_final: 0.8060 (mmm) REVERT: K 26 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7581 (mtm110) REVERT: J 122 THR cc_start: 0.9114 (m) cc_final: 0.8751 (p) outliers start: 136 outliers final: 66 residues processed: 546 average time/residue: 0.6845 time to fit residues: 452.7560 Evaluate side-chains 517 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 436 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 270 optimal weight: 5.9990 chunk 189 optimal weight: 0.0270 chunk 292 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 overall best weight: 2.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.071995 restraints weight = 50954.025| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.26 r_work: 0.2879 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38748 Z= 0.391 Angle : 2.481 50.637 52579 Z= 1.426 Chirality : 0.442 6.492 5841 Planarity : 0.004 0.071 6554 Dihedral : 8.650 136.417 5774 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.73 % Allowed : 17.86 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 4711 helix: 1.57 (0.10), residues: 2690 sheet: 0.00 (0.30), residues: 295 loop : -0.39 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 198 TYR 0.022 0.002 TYR N 424 PHE 0.026 0.001 PHE L 341 TRP 0.022 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01134 (38712) covalent geometry : angle 2.16099 (52486) hydrogen bonds : bond 0.04914 ( 1708) hydrogen bonds : angle 4.06793 ( 5124) metal coordination : bond 0.03805 ( 36) metal coordination : angle 29.06817 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 454 time to evaluate : 1.532 Fit side-chains REVERT: F 307 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8584 (mp) REVERT: F 373 ARG cc_start: 0.8077 (mpp80) cc_final: 0.7461 (mtm-85) REVERT: G 98 MET cc_start: 0.9139 (mmp) cc_final: 0.8668 (mmp) REVERT: G 490 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8210 (tp40) REVERT: G 541 MET cc_start: 0.8866 (mmt) cc_final: 0.8397 (mmt) REVERT: G 670 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7661 (tm130) REVERT: G 834 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: C 127 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8818 (t80) REVERT: C 219 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.5982 (t0) REVERT: C 276 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 84 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7984 (pp20) REVERT: B 126 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8546 (ttt) REVERT: B 166 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (mtt) REVERT: I 126 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8525 (mtpp) REVERT: H 140 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7429 (pptt) REVERT: H 286 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6652 (tmt90) REVERT: A 29 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 108 PHE cc_start: 0.8715 (t80) cc_final: 0.8510 (t80) REVERT: L 40 LEU cc_start: 0.8889 (mp) cc_final: 0.8544 (mt) REVERT: L 199 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: L 241 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6780 (t0) REVERT: L 258 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.6677 (tmm) REVERT: L 318 TYR cc_start: 0.8241 (m-80) cc_final: 0.7261 (t80) REVERT: L 353 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6539 (mp) REVERT: L 546 ASP cc_start: 0.8078 (t70) cc_final: 0.7594 (t0) REVERT: M 291 MET cc_start: 0.8957 (mtp) cc_final: 0.8686 (mtp) REVERT: M 303 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.6865 (m-10) REVERT: M 384 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8455 (tt) REVERT: M 447 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: N 388 MET cc_start: 0.7961 (mtm) cc_final: 0.7442 (mtp) REVERT: K 26 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7569 (mtm110) REVERT: J 122 THR cc_start: 0.9101 (m) cc_final: 0.8757 (p) outliers start: 145 outliers final: 68 residues processed: 549 average time/residue: 0.7055 time to fit residues: 469.0945 Evaluate side-chains 531 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 442 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 462 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 357 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069400 restraints weight = 50584.586| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.23 r_work: 0.2818 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38748 Z= 0.438 Angle : 2.498 50.620 52579 Z= 1.434 Chirality : 0.446 6.607 5841 Planarity : 0.005 0.066 6554 Dihedral : 9.041 137.726 5774 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 3.78 % Allowed : 17.96 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.91 (0.12), residues: 4711 helix: 1.40 (0.10), residues: 2688 sheet: -0.09 (0.29), residues: 294 loop : -0.46 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 198 TYR 0.023 0.002 TYR K 52 PHE 0.026 0.002 PHE N 251 TRP 0.022 0.002 TRP J 93 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01222 (38712) covalent geometry : angle 2.18218 (52486) hydrogen bonds : bond 0.05879 ( 1708) hydrogen bonds : angle 4.28329 ( 5124) metal coordination : bond 0.05348 ( 36) metal coordination : angle 28.98347 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 447 time to evaluate : 1.246 Fit side-chains REVERT: F 417 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8024 (pp20) REVERT: G 490 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: G 541 MET cc_start: 0.8882 (mmt) cc_final: 0.8324 (mmt) REVERT: G 834 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: C 112 MET cc_start: 0.8815 (ttm) cc_final: 0.8580 (ttm) REVERT: C 190 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (tp40) REVERT: C 232 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8008 (mtm180) REVERT: C 240 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: B 166 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8606 (mtt) REVERT: I 126 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8526 (mtpp) REVERT: H 140 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7534 (pptt) REVERT: H 286 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.6647 (tmt90) REVERT: A 29 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8426 (mm) REVERT: L 40 LEU cc_start: 0.8925 (mp) cc_final: 0.8558 (mt) REVERT: L 199 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: L 353 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6570 (mp) REVERT: L 427 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (mt) REVERT: L 546 ASP cc_start: 0.8102 (t70) cc_final: 0.7894 (t0) REVERT: L 578 PHE cc_start: 0.7492 (t80) cc_final: 0.7115 (t80) REVERT: M 291 MET cc_start: 0.8966 (mtp) cc_final: 0.8724 (mtp) REVERT: M 303 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: M 384 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8481 (tt) REVERT: M 447 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7128 (mtpt) REVERT: N 379 MET cc_start: 0.9118 (mmt) cc_final: 0.8850 (mmt) REVERT: K 26 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7628 (mtm110) REVERT: J 122 THR cc_start: 0.9108 (m) cc_final: 0.8736 (p) outliers start: 147 outliers final: 76 residues processed: 544 average time/residue: 0.7312 time to fit residues: 479.2859 Evaluate side-chains 523 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 52 optimal weight: 0.6980 chunk 373 optimal weight: 10.0000 chunk 381 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072363 restraints weight = 50860.402| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.25 r_work: 0.2876 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38748 Z= 0.388 Angle : 2.483 50.692 52579 Z= 1.426 Chirality : 0.441 6.468 5841 Planarity : 0.004 0.071 6554 Dihedral : 8.738 137.486 5771 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.99 % Allowed : 18.94 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.14 (0.12), residues: 4711 helix: 1.59 (0.10), residues: 2687 sheet: -0.04 (0.30), residues: 299 loop : -0.37 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 198 TYR 0.023 0.002 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.027 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01129 (38712) covalent geometry : angle 2.16219 (52486) hydrogen bonds : bond 0.04904 ( 1708) hydrogen bonds : angle 4.10877 ( 5124) metal coordination : bond 0.03439 ( 36) metal coordination : angle 29.11485 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 463 time to evaluate : 1.422 Fit side-chains REVERT: F 373 ARG cc_start: 0.8054 (mpp80) cc_final: 0.7370 (mtm-85) REVERT: F 417 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8017 (pp20) REVERT: G 541 MET cc_start: 0.8866 (mmt) cc_final: 0.8423 (mmt) REVERT: G 834 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.6879 (mp10) REVERT: C 127 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8836 (t80) REVERT: C 232 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8043 (mtm180) REVERT: C 240 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 166 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8580 (mtt) REVERT: I 126 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8550 (mtpp) REVERT: I 169 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7983 (mt-10) REVERT: H 286 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6673 (tmt90) REVERT: A 31 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8766 (mp) REVERT: L 40 LEU cc_start: 0.8897 (mp) cc_final: 0.8578 (mt) REVERT: L 199 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: L 318 TYR cc_start: 0.8256 (m-80) cc_final: 0.7209 (t80) REVERT: L 546 ASP cc_start: 0.8092 (t70) cc_final: 0.7575 (t0) REVERT: M 291 MET cc_start: 0.8937 (mtp) cc_final: 0.8671 (mtp) REVERT: M 303 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: M 384 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8476 (tt) REVERT: M 447 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7167 (mtpt) REVERT: N 379 MET cc_start: 0.9046 (mmt) cc_final: 0.8766 (mmt) REVERT: N 388 MET cc_start: 0.7965 (mtm) cc_final: 0.7520 (mtp) REVERT: J 122 THR cc_start: 0.9095 (m) cc_final: 0.8754 (p) outliers start: 116 outliers final: 53 residues processed: 542 average time/residue: 0.7324 time to fit residues: 477.9038 Evaluate side-chains 507 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 441 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 446 optimal weight: 0.9980 chunk 410 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 424 optimal weight: 0.7980 chunk 355 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 839 GLN G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071714 restraints weight = 50530.017| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.24 r_work: 0.2863 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38748 Z= 0.398 Angle : 2.487 50.653 52579 Z= 1.429 Chirality : 0.443 6.518 5841 Planarity : 0.004 0.070 6554 Dihedral : 8.775 137.714 5771 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.73 % Allowed : 19.76 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.12 (0.12), residues: 4711 helix: 1.56 (0.10), residues: 2688 sheet: -0.01 (0.30), residues: 298 loop : -0.36 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 198 TYR 0.027 0.002 TYR K 52 PHE 0.026 0.001 PHE L 341 TRP 0.028 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01148 (38712) covalent geometry : angle 2.16869 (52486) hydrogen bonds : bond 0.05152 ( 1708) hydrogen bonds : angle 4.14471 ( 5124) metal coordination : bond 0.04051 ( 36) metal coordination : angle 29.03111 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 446 time to evaluate : 1.417 Fit side-chains REVERT: F 417 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: G 490 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: G 541 MET cc_start: 0.8863 (mmt) cc_final: 0.8380 (mmt) REVERT: G 834 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: C 127 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8867 (t80) REVERT: C 232 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8091 (mtm180) REVERT: C 240 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: B 166 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (mtt) REVERT: I 126 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8511 (mtpp) REVERT: I 169 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8001 (mt-10) REVERT: H 286 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6674 (tmt90) REVERT: L 40 LEU cc_start: 0.8902 (mp) cc_final: 0.8587 (mt) REVERT: L 546 ASP cc_start: 0.8090 (t70) cc_final: 0.7590 (t0) REVERT: M 90 MET cc_start: 0.8451 (mmt) cc_final: 0.8119 (mmt) REVERT: M 291 MET cc_start: 0.8945 (mtp) cc_final: 0.8673 (mtp) REVERT: M 303 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.6878 (m-10) REVERT: M 384 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8477 (tt) REVERT: M 447 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7179 (mtpt) REVERT: N 323 MET cc_start: 0.7790 (mpt) cc_final: 0.7511 (mtm) REVERT: N 379 MET cc_start: 0.8989 (mmt) cc_final: 0.8492 (mmt) REVERT: J 122 THR cc_start: 0.9106 (m) cc_final: 0.8788 (p) outliers start: 106 outliers final: 60 residues processed: 522 average time/residue: 0.7307 time to fit residues: 460.9509 Evaluate side-chains 508 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 436 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 463 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 424 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 415 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 839 GLN G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070734 restraints weight = 50758.662| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.25 r_work: 0.2841 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38748 Z= 0.415 Angle : 2.494 50.636 52579 Z= 1.432 Chirality : 0.445 6.556 5841 Planarity : 0.005 0.148 6554 Dihedral : 8.964 138.745 5770 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 19.69 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.00 (0.12), residues: 4711 helix: 1.47 (0.10), residues: 2689 sheet: -0.07 (0.29), residues: 298 loop : -0.41 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 198 TYR 0.025 0.002 TYR K 52 PHE 0.026 0.002 PHE L 341 TRP 0.032 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01177 (38712) covalent geometry : angle 2.17778 (52486) hydrogen bonds : bond 0.05533 ( 1708) hydrogen bonds : angle 4.23233 ( 5124) metal coordination : bond 0.04802 ( 36) metal coordination : angle 28.98209 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 439 time to evaluate : 1.522 Fit side-chains REVERT: F 417 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8030 (pp20) REVERT: G 490 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8205 (tp40) REVERT: G 541 MET cc_start: 0.8878 (mmt) cc_final: 0.8390 (mmt) REVERT: G 834 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: G 837 MET cc_start: 0.8707 (mtp) cc_final: 0.8484 (ttp) REVERT: C 112 MET cc_start: 0.8840 (ttm) cc_final: 0.8625 (ttm) REVERT: C 127 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8937 (t80) REVERT: C 240 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: B 84 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: I 126 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8528 (mtpp) REVERT: I 169 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8087 (mt-10) REVERT: H 286 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6664 (tmt90) REVERT: A 125 TRP cc_start: 0.7537 (t-100) cc_final: 0.7335 (t-100) REVERT: L 40 LEU cc_start: 0.8914 (mp) cc_final: 0.8545 (mt) REVERT: L 427 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8311 (mt) REVERT: L 546 ASP cc_start: 0.8122 (t70) cc_final: 0.7615 (t0) REVERT: L 578 PHE cc_start: 0.7493 (t80) cc_final: 0.7123 (t80) REVERT: M 291 MET cc_start: 0.8956 (mtp) cc_final: 0.8695 (mtp) REVERT: M 303 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.6894 (m-10) REVERT: M 345 MET cc_start: 0.8199 (ptp) cc_final: 0.7992 (ptp) REVERT: M 384 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8490 (tt) REVERT: M 418 VAL cc_start: 0.7734 (m) cc_final: 0.7511 (p) REVERT: M 447 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7149 (mtpt) REVERT: N 379 MET cc_start: 0.8982 (mmt) cc_final: 0.8529 (mmt) REVERT: N 388 MET cc_start: 0.8064 (mtm) cc_final: 0.7612 (mtp) REVERT: J 109 TYR cc_start: 0.8346 (t80) cc_final: 0.8072 (t80) REVERT: J 122 THR cc_start: 0.9110 (m) cc_final: 0.8756 (p) outliers start: 103 outliers final: 61 residues processed: 513 average time/residue: 0.7549 time to fit residues: 463.4749 Evaluate side-chains 503 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 430 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 93 optimal weight: 10.0000 chunk 428 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 364 optimal weight: 8.9990 chunk 372 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 283 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 839 GLN G 901 HIS C 228 HIS B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073713 restraints weight = 50839.583| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.24 r_work: 0.2900 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38748 Z= 0.384 Angle : 2.486 50.682 52579 Z= 1.427 Chirality : 0.440 6.421 5841 Planarity : 0.004 0.074 6554 Dihedral : 8.596 137.801 5770 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.90 % Allowed : 20.56 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.25 (0.12), residues: 4711 helix: 1.68 (0.10), residues: 2684 sheet: 0.02 (0.30), residues: 298 loop : -0.30 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 198 TYR 0.026 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.036 0.001 TRP J 93 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01124 (38712) covalent geometry : angle 2.16449 (52486) hydrogen bonds : bond 0.04631 ( 1708) hydrogen bonds : angle 4.06079 ( 5124) metal coordination : bond 0.02889 ( 36) metal coordination : angle 29.15488 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 459 time to evaluate : 1.442 Fit side-chains REVERT: F 373 ARG cc_start: 0.7946 (mpp80) cc_final: 0.7430 (mtm-85) REVERT: G 541 MET cc_start: 0.8882 (mmt) cc_final: 0.8481 (mmt) REVERT: G 727 ARG cc_start: 0.7617 (tpt-90) cc_final: 0.7369 (tpt-90) REVERT: G 834 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: C 232 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7981 (mtm180) REVERT: C 240 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: B 126 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8563 (ttt) REVERT: I 126 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8551 (mtpp) REVERT: I 169 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 125 TRP cc_start: 0.7350 (t-100) cc_final: 0.7144 (t-100) REVERT: L 40 LEU cc_start: 0.8878 (mp) cc_final: 0.8574 (mt) REVERT: L 546 ASP cc_start: 0.8097 (t70) cc_final: 0.7585 (t0) REVERT: M 90 MET cc_start: 0.8390 (mmt) cc_final: 0.8091 (mmt) REVERT: M 291 MET cc_start: 0.8884 (mtp) cc_final: 0.8650 (mtp) REVERT: M 303 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.6847 (m-10) REVERT: M 345 MET cc_start: 0.8116 (ptp) cc_final: 0.7855 (ptm) REVERT: M 367 HIS cc_start: 0.8381 (m-70) cc_final: 0.8013 (m-70) REVERT: M 384 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8475 (tt) REVERT: M 414 SER cc_start: 0.8515 (t) cc_final: 0.8202 (p) REVERT: M 447 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7158 (mtpt) REVERT: N 323 MET cc_start: 0.7663 (mpt) cc_final: 0.7415 (mtm) REVERT: N 379 MET cc_start: 0.8910 (mmt) cc_final: 0.8477 (mmt) REVERT: N 388 MET cc_start: 0.7847 (mtm) cc_final: 0.7302 (mtt) REVERT: K 26 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7744 (mtm110) REVERT: J 122 THR cc_start: 0.9110 (m) cc_final: 0.8780 (p) outliers start: 74 outliers final: 46 residues processed: 516 average time/residue: 0.7600 time to fit residues: 471.7082 Evaluate side-chains 493 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 310 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 461 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 404 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 302 optimal weight: 0.0170 chunk 357 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 839 GLN G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072695 restraints weight = 50789.918| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.23 r_work: 0.2889 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38748 Z= 0.387 Angle : 2.486 50.640 52579 Z= 1.428 Chirality : 0.441 6.457 5841 Planarity : 0.004 0.074 6554 Dihedral : 8.526 137.497 5767 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.98 % Allowed : 20.41 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.28 (0.12), residues: 4711 helix: 1.69 (0.10), residues: 2685 sheet: 0.05 (0.30), residues: 298 loop : -0.28 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 198 TYR 0.024 0.002 TYR M 435 PHE 0.026 0.001 PHE L 341 TRP 0.037 0.001 TRP J 93 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01128 (38712) covalent geometry : angle 2.16630 (52486) hydrogen bonds : bond 0.04742 ( 1708) hydrogen bonds : angle 4.04791 ( 5124) metal coordination : bond 0.03285 ( 36) metal coordination : angle 29.06537 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15116.33 seconds wall clock time: 257 minutes 10.91 seconds (15430.91 seconds total)