Starting phenix.real_space_refine on Wed Feb 14 05:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d6x_30595/02_2024/7d6x_30595_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.058 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: 6 Type Number sf(0) Gaussians Fe 11 7.16 5 P 3 5.49 5 S 63 5.16 5 C 5510 2.51 5 N 1527 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8711 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4531 Classifications: {'peptide': 594} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 28, 'TRANS': 565} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1914 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 225} 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: "C" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2141 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'FES': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4955 SG CYS B 54 40.180 50.828 44.564 1.00 47.83 S ATOM 4988 SG CYS B 59 43.330 52.111 45.865 1.00 44.04 S ATOM 5004 SG CYS B 62 40.040 56.787 49.369 1.00 38.59 S ATOM 5095 SG CYS B 74 37.355 54.005 48.548 1.00 44.78 S ATOM 5724 SG CYS B 151 49.821 52.122 59.823 1.00 33.32 S ATOM 5676 SG CYS B 145 48.703 47.346 55.630 1.00 37.11 S ATOM 5699 SG CYS B 148 45.322 53.550 55.841 1.00 34.94 S ATOM 6224 SG CYS B 213 43.207 48.452 59.497 1.00 36.21 S ATOM 6151 SG CYS B 203 52.826 51.709 70.220 1.00 35.58 S ATOM 5754 SG CYS B 155 52.970 56.300 66.188 1.00 35.44 S ATOM 6195 SG CYS B 209 47.472 51.268 66.441 1.00 37.85 S ATOM 8037 SG CYS C 206 48.119 40.050 81.592 1.00 37.27 S ATOM 7292 SG CYS C 114 45.646 46.687 82.164 1.00 36.54 S Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8711 At special positions: 0 Unit cell: (84.46, 88.56, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 11 26.01 S 63 16.00 P 3 15.00 O 1597 8.00 N 1527 7.00 C 5510 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 203 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 155 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 209 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 59 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 62 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 74 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 54 " pdb=" FES C 302 " pdb="FE1 FES C 302 " - pdb=" NE2 HIS C 155 " pdb="FE2 FES C 302 " - pdb=" NE2 HIS C 240 " pdb="FE2 FES C 302 " - pdb=" SG CYS C 114 " pdb="FE1 FES C 302 " - pdb=" SG CYS C 206 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 213 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 151 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 148 " Number of angles added : 29 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 39.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 46 through 49 Processing helix chain 'A' and resid 67 through 77 Processing helix chain 'A' and resid 84 through 101 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.943A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.448A pdb=" N ASP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 502 through 505 No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 507 through 521 removed outlier: 3.835A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 556 removed outlier: 4.376A pdb=" N ARG A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 removed outlier: 4.427A pdb=" N LYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 133 through 144 removed outlier: 4.733A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.704A pdb=" N ILE B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.775A pdb=" N GLN B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.631A pdb=" N ARG B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 55 removed outlier: 3.760A pdb=" N PHE C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.674A pdb=" N LYS C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 147 through 175 removed outlier: 3.803A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLN C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N HIS C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR C 157 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 224 through 263 removed outlier: 4.560A pdb=" N ARG C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.686A pdb=" N TYR A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE A 174 " --> pdb=" O TYR A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 204 through 206 Processing sheet with id= C, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= D, first strand: chain 'A' and resid 246 through 249 removed outlier: 6.444A pdb=" N HIS A 249 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N CYS A 387 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 17 through 27 removed outlier: 3.548A pdb=" N ASP B 14 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 63 through 65 282 hydrogen bonds defined for protein. 828 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: 2.44 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 8823 1.74 - 2.31: 104 2.31 - 2.87: 0 2.87 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8930 Sorted by residual: bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 4.001 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.925 -1.667 2.00e-02 2.50e+03 6.95e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.729 -1.496 2.00e-02 2.50e+03 5.60e+03 bond pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.296 2.048 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" S2 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.317 2.083 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 42.74 - 63.88: 6 63.88 - 85.02: 5 85.02 - 106.16: 298 106.16 - 127.30: 11700 127.30 - 148.44: 123 Bond angle restraints: 12132 Sorted by residual: angle pdb=" N CYS B 54 " pdb=" CA CYS B 54 " pdb=" C CYS B 54 " ideal model delta sigma weight residual 114.12 148.44 -34.32 1.39e+00 5.18e-01 6.10e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 49.01 65.74 3.00e+00 1.11e-01 4.80e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 50.99 61.60 3.00e+00 1.11e-01 4.22e+02 angle pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta sigma weight residual 111.54 83.03 28.51 1.45e+00 4.76e-01 3.87e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 89.91 14.42 1.14e+00 7.69e-01 1.60e+02 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 5043 27.08 - 54.17: 233 54.17 - 81.25: 22 81.25 - 108.33: 4 108.33 - 135.41: 1 Dihedral angle restraints: 5303 sinusoidal: 2161 harmonic: 3142 Sorted by residual: dihedral pdb=" C CYS B 59 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual -122.60 -158.19 35.59 0 2.50e+00 1.60e-01 2.03e+02 dihedral pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " ideal model delta harmonic sigma weight residual 122.80 158.28 -35.48 0 2.50e+00 1.60e-01 2.01e+02 dihedral pdb=" N LYS B 58 " pdb=" C LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta harmonic sigma weight residual 122.80 89.09 33.71 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.902: 1316 2.902 - 5.804: 0 5.804 - 8.706: 0 8.706 - 11.607: 0 11.607 - 14.509: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -3.74 14.51 2.00e-01 2.50e+01 5.26e+03 chirality pdb=" CA CYS B 59 " pdb=" N CYS B 59 " pdb=" C CYS B 59 " pdb=" CB CYS B 59 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.89e+01 chirality pdb=" CA LYS B 55 " pdb=" N LYS B 55 " pdb=" C LYS B 55 " pdb=" CB LYS B 55 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 1314 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 606 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 607 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 128 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 129 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 145 " 0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C CYS B 145 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS B 145 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE B 146 " 0.020 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.15: 7040 3.15 - 3.74: 13145 3.74 - 4.32: 20193 4.32 - 4.90: 33408 Nonbonded interactions: 73868 Sorted by model distance: nonbonded pdb=" O2' FAD A 701 " pdb=" O4' FAD A 701 " model vdw 1.988 2.440 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.052 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.088 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.130 2.688 nonbonded pdb=" OD1 ASP B 237 " pdb=" OH TYR C 157 " model vdw 2.202 2.440 ... (remaining 73863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.320 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: 0.010 Extract box with map and model: 12.030 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.032 1.701 8930 Z= 2.027 Angle : 1.735 65.736 12132 Z= 0.891 Chirality : 0.412 14.509 1317 Planarity : 0.007 0.112 1560 Dihedral : 14.906 135.413 3293 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.66 % Favored : 88.06 % Rotamer: Outliers : 0.22 % Allowed : 5.11 % Favored : 94.67 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1089 helix: -0.81 (0.24), residues: 425 sheet: -1.32 (0.51), residues: 92 loop : -3.03 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 55 HIS 0.008 0.001 HIS A 170 PHE 0.022 0.002 PHE A 530 TYR 0.023 0.002 TYR B 202 ARG 0.005 0.001 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.971 Fit side-chains REVERT: A 366 HIS cc_start: 0.7613 (m90) cc_final: 0.7228 (p-80) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 1.4907 time to fit residues: 179.5076 Evaluate side-chains 79 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.0170 chunk 98 optimal weight: 0.0010 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 330 ASN A 480 ASN B 133 GLN B 195 GLN C 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8930 Z= 0.184 Angle : 1.052 85.100 12132 Z= 0.420 Chirality : 0.058 1.383 1317 Planarity : 0.006 0.110 1560 Dihedral : 9.867 115.242 1310 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 2.00 % Allowed : 11.78 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1089 helix: 0.22 (0.26), residues: 430 sheet: -1.10 (0.57), residues: 76 loop : -2.65 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.002 0.000 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.024 0.001 TYR C 121 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.969 Fit side-chains REVERT: A 112 LYS cc_start: 0.8236 (tppt) cc_final: 0.7796 (mppt) REVERT: A 366 HIS cc_start: 0.7586 (m90) cc_final: 0.7292 (p-80) REVERT: A 441 LEU cc_start: 0.8215 (tt) cc_final: 0.7667 (tt) REVERT: A 445 ASP cc_start: 0.7925 (m-30) cc_final: 0.7627 (m-30) REVERT: A 603 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 69 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8065 (mmm-85) REVERT: B 211 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7703 (mm-30) outliers start: 18 outliers final: 5 residues processed: 104 average time/residue: 1.2286 time to fit residues: 136.8827 Evaluate side-chains 87 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 211 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8930 Z= 0.270 Angle : 1.043 82.179 12132 Z= 0.422 Chirality : 0.061 1.504 1317 Planarity : 0.006 0.103 1560 Dihedral : 8.987 108.100 1310 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.67 % Allowed : 13.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 1089 helix: 0.58 (0.27), residues: 426 sheet: -0.90 (0.57), residues: 76 loop : -2.47 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 PHE 0.015 0.001 PHE A 435 TYR 0.022 0.001 TYR C 121 ARG 0.004 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.989 Fit side-chains REVERT: A 366 HIS cc_start: 0.7658 (m90) cc_final: 0.7267 (p-80) REVERT: A 441 LEU cc_start: 0.8264 (tt) cc_final: 0.7691 (tt) REVERT: A 445 ASP cc_start: 0.7960 (m-30) cc_final: 0.7690 (m-30) REVERT: A 502 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 572 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5116 (pp-130) REVERT: B 69 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8063 (mmm-85) REVERT: B 110 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: C 235 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7962 (mtmp) REVERT: C 269 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5150 (mp) outliers start: 24 outliers final: 9 residues processed: 102 average time/residue: 1.1967 time to fit residues: 130.7614 Evaluate side-chains 94 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8930 Z= 0.228 Angle : 1.020 81.434 12132 Z= 0.408 Chirality : 0.061 1.540 1317 Planarity : 0.005 0.095 1560 Dihedral : 8.198 100.420 1310 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.44 % Allowed : 14.00 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 1089 helix: 0.65 (0.27), residues: 440 sheet: -1.05 (0.56), residues: 81 loop : -2.39 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.021 0.001 TYR C 121 ARG 0.003 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.059 Fit side-chains REVERT: A 366 HIS cc_start: 0.7644 (m90) cc_final: 0.7221 (p-80) REVERT: A 441 LEU cc_start: 0.8233 (tt) cc_final: 0.7661 (tt) REVERT: A 445 ASP cc_start: 0.7986 (m-30) cc_final: 0.7725 (m-30) REVERT: A 502 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 572 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5175 (pp-130) REVERT: A 606 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.4423 (ptt90) REVERT: B 69 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8001 (mmm-85) REVERT: B 110 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: C 235 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7981 (mtmp) REVERT: C 259 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (ttm) REVERT: C 269 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5088 (mp) outliers start: 31 outliers final: 14 residues processed: 111 average time/residue: 1.2537 time to fit residues: 148.6892 Evaluate side-chains 101 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 8930 Z= 0.330 Angle : 1.051 80.764 12132 Z= 0.429 Chirality : 0.063 1.559 1317 Planarity : 0.006 0.092 1560 Dihedral : 8.283 98.222 1310 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.78 % Allowed : 14.78 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.26), residues: 1089 helix: 0.75 (0.27), residues: 427 sheet: -0.91 (0.57), residues: 81 loop : -2.34 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 95 HIS 0.006 0.001 HIS A 170 PHE 0.016 0.002 PHE B 173 TYR 0.021 0.001 TYR C 121 ARG 0.004 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 0.955 Fit side-chains REVERT: A 366 HIS cc_start: 0.7687 (m90) cc_final: 0.7247 (p-80) REVERT: A 441 LEU cc_start: 0.8295 (tt) cc_final: 0.7732 (tt) REVERT: A 445 ASP cc_start: 0.8025 (m-30) cc_final: 0.7763 (m-30) REVERT: A 502 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 572 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.6008 (ppp) REVERT: A 612 CYS cc_start: 0.2738 (OUTLIER) cc_final: 0.0630 (m) REVERT: B 69 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8131 (mmm-85) REVERT: B 110 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: B 221 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: C 185 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7658 (t80) REVERT: C 235 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8003 (mtmp) REVERT: C 259 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7519 (ttm) REVERT: C 269 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5190 (mp) outliers start: 34 outliers final: 16 residues processed: 107 average time/residue: 1.1871 time to fit residues: 136.0773 Evaluate side-chains 103 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8930 Z= 0.233 Angle : 1.026 81.230 12132 Z= 0.413 Chirality : 0.061 1.552 1317 Planarity : 0.005 0.090 1560 Dihedral : 7.878 93.821 1310 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.78 % Allowed : 14.89 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.26), residues: 1089 helix: 0.81 (0.27), residues: 435 sheet: -0.95 (0.56), residues: 81 loop : -2.30 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.004 0.001 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 85 time to evaluate : 1.057 Fit side-chains REVERT: A 445 ASP cc_start: 0.7979 (m-30) cc_final: 0.7709 (m-30) REVERT: A 502 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 572 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5766 (ppp) REVERT: A 612 CYS cc_start: 0.2390 (OUTLIER) cc_final: 0.0602 (m) REVERT: B 69 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7992 (mmm-85) REVERT: C 185 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7664 (t80) REVERT: C 235 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7968 (mtmp) REVERT: C 259 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7478 (ttm) REVERT: C 269 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5171 (mp) outliers start: 34 outliers final: 15 residues processed: 113 average time/residue: 1.1784 time to fit residues: 142.7213 Evaluate side-chains 100 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8930 Z= 0.267 Angle : 1.036 81.052 12132 Z= 0.419 Chirality : 0.062 1.558 1317 Planarity : 0.005 0.089 1560 Dihedral : 7.857 92.230 1310 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 4.22 % Allowed : 15.00 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1089 helix: 0.82 (0.27), residues: 435 sheet: -0.91 (0.56), residues: 81 loop : -2.29 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 95 HIS 0.005 0.001 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.003 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 1.062 Fit side-chains REVERT: A 441 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 462 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6893 (pt0) REVERT: A 502 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 572 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5853 (ppp) REVERT: A 612 CYS cc_start: 0.2502 (OUTLIER) cc_final: 0.0565 (m) REVERT: B 69 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8053 (mmm-85) REVERT: C 185 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7741 (t80) REVERT: C 235 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7951 (mtmp) REVERT: C 259 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7479 (ttm) REVERT: C 269 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5138 (mp) outliers start: 38 outliers final: 20 residues processed: 106 average time/residue: 1.2599 time to fit residues: 142.7409 Evaluate side-chains 102 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8930 Z= 0.192 Angle : 1.014 81.609 12132 Z= 0.404 Chirality : 0.060 1.545 1317 Planarity : 0.005 0.090 1560 Dihedral : 7.414 88.615 1310 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.56 % Allowed : 15.56 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.26), residues: 1089 helix: 0.97 (0.27), residues: 435 sheet: -0.96 (0.56), residues: 81 loop : -2.17 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.002 0.000 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.003 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 0.920 Fit side-chains REVERT: A 502 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 572 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5753 (ppp) REVERT: A 612 CYS cc_start: 0.1855 (OUTLIER) cc_final: 0.0370 (m) REVERT: C 185 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 235 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7937 (mtmp) REVERT: C 259 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7445 (ttm) REVERT: C 269 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5204 (mp) outliers start: 32 outliers final: 14 residues processed: 110 average time/residue: 1.1734 time to fit residues: 138.1015 Evaluate side-chains 100 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8930 Z= 0.190 Angle : 1.011 81.687 12132 Z= 0.401 Chirality : 0.060 1.540 1317 Planarity : 0.005 0.096 1560 Dihedral : 7.131 86.204 1310 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1089 helix: 1.09 (0.27), residues: 436 sheet: -0.76 (0.58), residues: 76 loop : -2.14 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.002 0.000 HIS A 170 PHE 0.013 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 1.030 Fit side-chains REVERT: A 502 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 572 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5560 (ppp) REVERT: A 612 CYS cc_start: 0.2097 (OUTLIER) cc_final: 0.0671 (m) REVERT: C 185 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7603 (t80) REVERT: C 235 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7942 (mtmp) REVERT: C 259 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7412 (ttm) REVERT: C 269 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5610 (mp) outliers start: 23 outliers final: 11 residues processed: 109 average time/residue: 1.2072 time to fit residues: 140.9220 Evaluate side-chains 99 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8930 Z= 0.197 Angle : 1.018 81.685 12132 Z= 0.405 Chirality : 0.060 1.541 1317 Planarity : 0.005 0.098 1560 Dihedral : 7.053 84.708 1310 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.89 % Allowed : 17.78 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1089 helix: 1.15 (0.27), residues: 436 sheet: -0.71 (0.58), residues: 76 loop : -2.10 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.002 0.000 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.973 Fit side-chains REVERT: A 502 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 572 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5684 (ppp) REVERT: A 612 CYS cc_start: 0.1976 (OUTLIER) cc_final: 0.0664 (m) REVERT: C 235 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7936 (mtmp) REVERT: C 259 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7421 (ttm) REVERT: C 269 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5415 (mp) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 1.1707 time to fit residues: 121.9658 Evaluate side-chains 94 residues out of total 913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0970 chunk 26 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100983 restraints weight = 12282.086| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.78 r_work: 0.3119 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8930 Z= 0.209 Angle : 1.015 81.551 12132 Z= 0.405 Chirality : 0.060 1.544 1317 Planarity : 0.005 0.100 1560 Dihedral : 7.076 83.552 1310 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.22 % Allowed : 17.11 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1089 helix: 1.15 (0.27), residues: 436 sheet: -0.69 (0.58), residues: 76 loop : -2.11 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 95 HIS 0.003 0.000 HIS A 170 PHE 0.014 0.001 PHE C 96 TYR 0.020 0.001 TYR C 121 ARG 0.004 0.000 ARG C 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.92 seconds wall clock time: 57 minutes 20.63 seconds (3440.63 seconds total)