Starting phenix.real_space_refine on Wed Feb 14 08:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg4_12170/02_2024/7bg4_12170_updated.pdb" } resolution = 4.2 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= 0.010 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 P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5724 2.51 5 N 1483 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8927 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4405 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4392 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {' MG': 1, 'ATP': 2, 'RHQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' MG': 1, 'RHQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.55, per 1000 atoms: 0.62 Number of scatterers: 8927 At special positions: 0 Unit cell: (75.26, 90.1, 137.8, 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) S 35 16.00 P 6 15.00 Mg 2 11.99 O 1677 8.00 N 1483 7.00 C 5724 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 59.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 29 through 57 Proline residue: A 47 - end of helix removed outlier: 4.183A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 108 removed outlier: 4.107A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.262A pdb=" N THR A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 125 through 156 removed outlier: 4.543A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 167 through 207 removed outlier: 5.016A pdb=" N LEU A 171 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 173 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.757A pdb=" N ALA A 178 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.745A pdb=" N SER A 192 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A 196 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA A 200 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 203 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 204 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 5.459A pdb=" N ARG A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 238 through 266 removed outlier: 3.509A pdb=" N SER A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 250 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 4.211A pdb=" N VAL A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 266 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 3.867A pdb=" N VAL A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.575A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 4.178A pdb=" N GLU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 321' Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.562A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 445 through 454 removed outlier: 4.182A pdb=" N GLU A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.829A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.778A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 565 removed outlier: 3.894A pdb=" N ALA A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.401A pdb=" N MET A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 23 through 57 removed outlier: 4.319A pdb=" N LYS B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 30 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 42 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.670A pdb=" N THR B 50 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 54 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 108 removed outlier: 4.453A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.809A pdb=" N THR B 117 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.558A pdb=" N SER B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 3.861A pdb=" N GLU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.517A pdb=" N ILE B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 173 through 208 removed outlier: 3.641A pdb=" N ALA B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.561A pdb=" N ARG B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 5.294A pdb=" N ARG B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.878A pdb=" N TYR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 267 removed outlier: 3.589A pdb=" N GLU B 243 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 245 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 247 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 250 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.938A pdb=" N VAL B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 321 removed outlier: 3.917A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix removed outlier: 3.629A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 321 " --> pdb=" O MET B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 433 through 438 removed outlier: 4.461A pdb=" N TYR B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 433 through 438' Processing helix chain 'B' and resid 445 through 455 removed outlier: 5.032A pdb=" N GLU B 449 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 481 through 494 removed outlier: 3.567A pdb=" N ARG B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 removed outlier: 4.115A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.224A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.979A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP B 583 " --> pdb=" O LYS B 579 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.665A pdb=" N THR A 397 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 531 through 533 removed outlier: 6.298A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 549 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.536A pdb=" N ALA B 362 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.867A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 864 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: 2.59 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2855 1.34 - 1.46: 1370 1.46 - 1.58: 4764 1.58 - 1.69: 10 1.69 - 1.81: 68 Bond restraints: 9067 Sorted by residual: bond pdb=" C2 RHQ A 604 " pdb=" C3 RHQ A 604 " ideal model delta sigma weight residual 1.158 1.435 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C2 RHQ B 602 " pdb=" C3 RHQ B 602 " ideal model delta sigma weight residual 1.158 1.434 -0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C1 RHQ A 604 " pdb=" C2 RHQ A 604 " ideal model delta sigma weight residual 1.200 1.405 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1 RHQ B 602 " pdb=" C2 RHQ B 602 " ideal model delta sigma weight residual 1.200 1.404 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C4 RHQ B 602 " pdb=" C5 RHQ B 602 " ideal model delta sigma weight residual 1.641 1.437 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 9062 not shown) Histogram of bond angle deviations from ideal: 94.95 - 103.28: 86 103.28 - 111.61: 4196 111.61 - 119.94: 4025 119.94 - 128.27: 3930 128.27 - 136.60: 49 Bond angle restraints: 12286 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.08 16.75 1.00e+00 1.00e+00 2.80e+02 angle pdb=" C6 RHQ B 602 " pdb=" C5 RHQ B 602 " pdb=" N2 RHQ B 602 " ideal model delta sigma weight residual 72.13 117.69 -45.56 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C6 RHQ A 604 " pdb=" C5 RHQ A 604 " pdb=" N2 RHQ A 604 " ideal model delta sigma weight residual 72.13 117.67 -45.54 3.00e+00 1.11e-01 2.30e+02 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4879 18.00 - 36.00: 500 36.00 - 54.00: 77 54.00 - 71.99: 15 71.99 - 89.99: 15 Dihedral angle restraints: 5486 sinusoidal: 2215 harmonic: 3271 Sorted by residual: dihedral pdb=" CA MET A 501 " pdb=" C MET A 501 " pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLU A 323 " pdb=" C GLU A 323 " pdb=" N GLU A 324 " pdb=" CA GLU A 324 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A 324 " pdb=" C GLU A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 5483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1324 0.077 - 0.154: 137 0.154 - 0.231: 4 0.231 - 0.307: 2 0.307 - 0.384: 2 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CB VAL A 540 " pdb=" CA VAL A 540 " pdb=" CG1 VAL A 540 " pdb=" CG2 VAL A 540 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ILE A 533 " pdb=" N ILE A 533 " pdb=" C ILE A 533 " pdb=" CB ILE A 533 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1466 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 RHQ A 604 " -0.051 2.00e-02 2.50e+03 2.84e-01 2.22e+03 pdb=" C2 RHQ A 604 " 0.099 2.00e-02 2.50e+03 pdb=" C21 RHQ A 604 " -0.102 2.00e-02 2.50e+03 pdb=" C24 RHQ A 604 " 0.717 2.00e-02 2.50e+03 pdb=" C3 RHQ A 604 " 0.075 2.00e-02 2.50e+03 pdb=" C4 RHQ A 604 " -0.089 2.00e-02 2.50e+03 pdb=" C5 RHQ A 604 " -0.236 2.00e-02 2.50e+03 pdb=" C6 RHQ A 604 " -0.220 2.00e-02 2.50e+03 pdb=" C9 RHQ A 604 " 0.261 2.00e-02 2.50e+03 pdb=" N2 RHQ A 604 " -0.406 2.00e-02 2.50e+03 pdb=" O1 RHQ A 604 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 RHQ B 602 " 0.051 2.00e-02 2.50e+03 2.84e-01 2.22e+03 pdb=" C2 RHQ B 602 " -0.099 2.00e-02 2.50e+03 pdb=" C21 RHQ B 602 " 0.102 2.00e-02 2.50e+03 pdb=" C24 RHQ B 602 " -0.716 2.00e-02 2.50e+03 pdb=" C3 RHQ B 602 " -0.075 2.00e-02 2.50e+03 pdb=" C4 RHQ B 602 " 0.088 2.00e-02 2.50e+03 pdb=" C5 RHQ B 602 " 0.237 2.00e-02 2.50e+03 pdb=" C6 RHQ B 602 " 0.220 2.00e-02 2.50e+03 pdb=" C9 RHQ B 602 " -0.261 2.00e-02 2.50e+03 pdb=" N2 RHQ B 602 " 0.406 2.00e-02 2.50e+03 pdb=" O1 RHQ B 602 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 251 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO A 252 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " -0.038 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 117 2.53 - 3.12: 7708 3.12 - 3.71: 13781 3.71 - 4.31: 18479 4.31 - 4.90: 28628 Nonbonded interactions: 68713 Sorted by model distance: nonbonded pdb=" O2B ATP A 602 " pdb="MG MG B 601 " model vdw 1.937 2.170 nonbonded pdb=" OG1 THR A 381 " pdb="MG MG A 603 " model vdw 1.978 2.170 nonbonded pdb=" OE1 GLN B 422 " pdb="MG MG B 601 " model vdw 1.999 2.170 nonbonded pdb=" O PRO B 252 " pdb=" OG SER B 255 " model vdw 2.098 2.440 nonbonded pdb=" OG SER A 424 " pdb=" OE1 GLN A 485 " model vdw 2.129 2.440 ... (remaining 68708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 269 or resid 282 through 586 or resid 603 throug \ h 604)) selection = (chain 'B' and (resid 9 through 269 or resid 282 through 586 or resid 601 throug \ h 602)) } 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 group one per residue 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: 0.560 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: 2.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.220 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.277 9067 Z= 0.628 Angle : 1.215 45.559 12286 Z= 0.655 Chirality : 0.049 0.384 1469 Planarity : 0.011 0.284 1526 Dihedral : 15.106 89.993 3382 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.21 % Allowed : 1.56 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.15 (0.25), residues: 1133 helix: -0.84 (0.22), residues: 589 sheet: -0.23 (0.77), residues: 51 loop : -2.26 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS B 338 PHE 0.012 0.002 PHE B 160 TYR 0.012 0.002 TYR B 570 ARG 0.007 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8594 (tp) cc_final: 0.8224 (tp) REVERT: A 314 THR cc_start: 0.8391 (m) cc_final: 0.7816 (t) REVERT: B 249 LEU cc_start: 0.8948 (tp) cc_final: 0.8739 (tp) REVERT: B 430 THR cc_start: 0.8209 (p) cc_final: 0.6331 (p) outliers start: 2 outliers final: 0 residues processed: 281 average time/residue: 0.1924 time to fit residues: 76.1652 Evaluate side-chains 193 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9067 Z= 0.206 Angle : 0.775 11.951 12286 Z= 0.385 Chirality : 0.044 0.166 1469 Planarity : 0.005 0.049 1526 Dihedral : 8.731 79.994 1295 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.31 % Allowed : 6.24 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.71 (0.25), residues: 1133 helix: -0.54 (0.21), residues: 605 sheet: -0.47 (0.74), residues: 46 loop : -1.92 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 413 HIS 0.010 0.001 HIS B 535 PHE 0.012 0.002 PHE B 189 TYR 0.025 0.002 TYR B 408 ARG 0.006 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8286 (p) cc_final: 0.8078 (t) REVERT: A 249 LEU cc_start: 0.9113 (tt) cc_final: 0.8912 (tt) REVERT: A 293 ILE cc_start: 0.9065 (pt) cc_final: 0.8690 (mp) REVERT: A 305 THR cc_start: 0.9293 (p) cc_final: 0.8578 (p) REVERT: A 460 PHE cc_start: 0.6044 (m-80) cc_final: 0.5842 (m-80) REVERT: B 122 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7131 (mm-30) REVERT: B 196 GLN cc_start: 0.8066 (tp40) cc_final: 0.7760 (tp40) REVERT: B 208 GLN cc_start: 0.6866 (pt0) cc_final: 0.6625 (pt0) REVERT: B 243 GLU cc_start: 0.8007 (pp20) cc_final: 0.7678 (pp20) REVERT: B 289 TYR cc_start: 0.7670 (m-80) cc_final: 0.7283 (m-80) REVERT: B 299 GLN cc_start: 0.8777 (tt0) cc_final: 0.8409 (tt0) outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.1823 time to fit residues: 65.0641 Evaluate side-chains 188 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9067 Z= 0.256 Angle : 0.727 11.687 12286 Z= 0.367 Chirality : 0.043 0.215 1469 Planarity : 0.005 0.045 1526 Dihedral : 8.586 89.114 1295 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.44 (0.25), residues: 1133 helix: -0.35 (0.21), residues: 617 sheet: -0.50 (0.73), residues: 46 loop : -1.75 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.007 0.001 HIS B 535 PHE 0.016 0.002 PHE A 74 TYR 0.016 0.002 TYR A 289 ARG 0.009 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.6794 (mmp) cc_final: 0.5693 (tpp) REVERT: A 208 GLN cc_start: 0.8014 (mt0) cc_final: 0.7394 (tm-30) REVERT: A 231 MET cc_start: 0.7376 (tmm) cc_final: 0.7066 (tmm) REVERT: A 237 PHE cc_start: 0.7548 (m-80) cc_final: 0.7283 (m-80) REVERT: A 249 LEU cc_start: 0.9164 (tt) cc_final: 0.8912 (tt) REVERT: A 293 ILE cc_start: 0.9227 (pt) cc_final: 0.8795 (mp) REVERT: A 428 SER cc_start: 0.8116 (p) cc_final: 0.7787 (p) REVERT: A 460 PHE cc_start: 0.6140 (m-80) cc_final: 0.5931 (m-80) REVERT: B 18 LEU cc_start: 0.8525 (tp) cc_final: 0.8307 (tp) REVERT: B 122 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 130 ASP cc_start: 0.6899 (m-30) cc_final: 0.6396 (m-30) REVERT: B 196 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7928 (tp40) REVERT: B 249 LEU cc_start: 0.8934 (tp) cc_final: 0.8650 (tp) REVERT: B 289 TYR cc_start: 0.7814 (m-80) cc_final: 0.7455 (m-80) REVERT: B 327 ASP cc_start: 0.7748 (t0) cc_final: 0.7527 (t0) REVERT: B 577 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8561 (mp10) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.1650 time to fit residues: 54.4687 Evaluate side-chains 185 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9067 Z= 0.228 Angle : 0.711 11.676 12286 Z= 0.354 Chirality : 0.043 0.165 1469 Planarity : 0.004 0.042 1526 Dihedral : 8.486 86.899 1295 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.17 (0.26), residues: 1133 helix: -0.15 (0.21), residues: 623 sheet: -0.09 (0.68), residues: 57 loop : -1.68 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 413 HIS 0.006 0.001 HIS B 535 PHE 0.019 0.002 PHE A 74 TYR 0.019 0.001 TYR A 289 ARG 0.006 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.7599 (m-80) cc_final: 0.7395 (m-80) REVERT: A 249 LEU cc_start: 0.9138 (tt) cc_final: 0.8790 (tt) REVERT: A 293 ILE cc_start: 0.9202 (pt) cc_final: 0.8799 (mp) REVERT: B 122 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 130 ASP cc_start: 0.6850 (m-30) cc_final: 0.6352 (m-30) REVERT: B 196 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7943 (tp40) REVERT: B 243 GLU cc_start: 0.8321 (pp20) cc_final: 0.8070 (pp20) REVERT: B 289 TYR cc_start: 0.7794 (m-80) cc_final: 0.7488 (m-80) REVERT: B 327 ASP cc_start: 0.7586 (t0) cc_final: 0.7356 (t0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1548 time to fit residues: 50.2319 Evaluate side-chains 178 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9067 Z= 0.176 Angle : 0.717 11.633 12286 Z= 0.345 Chirality : 0.042 0.150 1469 Planarity : 0.004 0.041 1526 Dihedral : 7.846 71.373 1295 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.88 (0.26), residues: 1133 helix: 0.06 (0.22), residues: 603 sheet: -0.18 (0.65), residues: 63 loop : -1.43 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 104 HIS 0.005 0.001 HIS B 535 PHE 0.021 0.001 PHE A 145 TYR 0.020 0.001 TYR A 289 ARG 0.004 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.7749 (t) cc_final: 0.7504 (t) REVERT: A 162 MET cc_start: 0.5994 (mmp) cc_final: 0.5248 (tpp) REVERT: A 208 GLN cc_start: 0.7930 (mt0) cc_final: 0.7410 (tm-30) REVERT: A 249 LEU cc_start: 0.9185 (tt) cc_final: 0.8892 (tt) REVERT: A 256 LEU cc_start: 0.9540 (pp) cc_final: 0.9213 (mp) REVERT: A 293 ILE cc_start: 0.9126 (pt) cc_final: 0.8713 (mp) REVERT: A 311 ILE cc_start: 0.8882 (mm) cc_final: 0.8643 (tp) REVERT: A 382 THR cc_start: 0.8570 (p) cc_final: 0.8328 (m) REVERT: B 109 LYS cc_start: 0.7619 (tppt) cc_final: 0.7180 (tppt) REVERT: B 122 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6987 (mm-30) REVERT: B 130 ASP cc_start: 0.6688 (m-30) cc_final: 0.6176 (m-30) REVERT: B 196 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7841 (tp40) REVERT: B 243 GLU cc_start: 0.8304 (pp20) cc_final: 0.8016 (pp20) REVERT: B 248 SER cc_start: 0.8803 (p) cc_final: 0.8413 (p) REVERT: B 249 LEU cc_start: 0.8949 (tp) cc_final: 0.8673 (tp) REVERT: B 289 TYR cc_start: 0.7785 (m-80) cc_final: 0.7396 (m-80) REVERT: B 327 ASP cc_start: 0.7373 (t0) cc_final: 0.7147 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1747 time to fit residues: 57.5759 Evaluate side-chains 189 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 196 GLN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9067 Z= 0.170 Angle : 0.718 11.625 12286 Z= 0.345 Chirality : 0.043 0.179 1469 Planarity : 0.004 0.042 1526 Dihedral : 7.355 55.982 1295 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.88 (0.26), residues: 1133 helix: 0.04 (0.22), residues: 613 sheet: 0.15 (0.71), residues: 57 loop : -1.46 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 141 PHE 0.021 0.001 PHE B 384 TYR 0.020 0.001 TYR A 289 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASN cc_start: 0.7931 (m110) cc_final: 0.7160 (m-40) REVERT: A 208 GLN cc_start: 0.7956 (mt0) cc_final: 0.7460 (tm-30) REVERT: A 249 LEU cc_start: 0.9191 (tt) cc_final: 0.8877 (tt) REVERT: A 293 ILE cc_start: 0.9140 (pt) cc_final: 0.8764 (mp) REVERT: A 297 MET cc_start: 0.8669 (mmp) cc_final: 0.8420 (mmm) REVERT: A 311 ILE cc_start: 0.8786 (mm) cc_final: 0.8564 (tp) REVERT: B 130 ASP cc_start: 0.6676 (m-30) cc_final: 0.6195 (m-30) REVERT: B 196 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7913 (tp40) REVERT: B 243 GLU cc_start: 0.8307 (pp20) cc_final: 0.8033 (pp20) REVERT: B 248 SER cc_start: 0.8779 (p) cc_final: 0.8375 (p) REVERT: B 289 TYR cc_start: 0.7739 (m-80) cc_final: 0.7386 (m-80) REVERT: B 468 PHE cc_start: 0.7266 (m-10) cc_final: 0.7043 (m-10) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1757 time to fit residues: 55.0718 Evaluate side-chains 190 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS B 89 ASN B 129 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9067 Z= 0.225 Angle : 0.708 11.606 12286 Z= 0.351 Chirality : 0.043 0.172 1469 Planarity : 0.004 0.045 1526 Dihedral : 7.372 57.195 1295 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.26), residues: 1133 helix: 0.11 (0.22), residues: 610 sheet: 0.17 (0.70), residues: 57 loop : -1.31 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 413 HIS 0.005 0.001 HIS B 535 PHE 0.026 0.002 PHE B 304 TYR 0.017 0.001 TYR A 289 ARG 0.006 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8108 (mt0) cc_final: 0.7578 (tm-30) REVERT: A 249 LEU cc_start: 0.9206 (tt) cc_final: 0.8910 (tt) REVERT: A 293 ILE cc_start: 0.9171 (pt) cc_final: 0.8782 (mp) REVERT: A 305 THR cc_start: 0.9358 (p) cc_final: 0.8671 (p) REVERT: A 311 ILE cc_start: 0.8845 (mm) cc_final: 0.8608 (tp) REVERT: B 130 ASP cc_start: 0.6738 (m-30) cc_final: 0.6263 (m-30) REVERT: B 196 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7848 (tp40) REVERT: B 203 THR cc_start: 0.8514 (p) cc_final: 0.8123 (t) REVERT: B 243 GLU cc_start: 0.8460 (pp20) cc_final: 0.8081 (pp20) REVERT: B 249 LEU cc_start: 0.8982 (tp) cc_final: 0.8739 (tp) REVERT: B 289 TYR cc_start: 0.7808 (m-80) cc_final: 0.7412 (m-80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1522 time to fit residues: 46.5872 Evaluate side-chains 171 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 129 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9067 Z= 0.180 Angle : 0.729 11.700 12286 Z= 0.351 Chirality : 0.044 0.285 1469 Planarity : 0.004 0.063 1526 Dihedral : 7.270 57.153 1295 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.77 (0.26), residues: 1133 helix: 0.17 (0.22), residues: 608 sheet: -0.10 (0.73), residues: 53 loop : -1.41 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.005 0.001 HIS A 535 PHE 0.018 0.001 PHE A 74 TYR 0.018 0.001 TYR A 289 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7993 (mt0) cc_final: 0.7553 (tm-30) REVERT: A 249 LEU cc_start: 0.9161 (tt) cc_final: 0.8875 (tt) REVERT: A 293 ILE cc_start: 0.9151 (pt) cc_final: 0.8762 (mp) REVERT: A 297 MET cc_start: 0.8663 (mmp) cc_final: 0.8427 (mmm) REVERT: A 311 ILE cc_start: 0.8833 (mm) cc_final: 0.8557 (tp) REVERT: B 122 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6687 (mm-30) REVERT: B 203 THR cc_start: 0.8393 (p) cc_final: 0.8075 (t) REVERT: B 243 GLU cc_start: 0.8381 (pp20) cc_final: 0.8020 (pp20) REVERT: B 289 TYR cc_start: 0.7752 (m-80) cc_final: 0.7406 (m-80) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1627 time to fit residues: 50.6578 Evaluate side-chains 181 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 129 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9067 Z= 0.177 Angle : 0.731 11.669 12286 Z= 0.351 Chirality : 0.044 0.259 1469 Planarity : 0.004 0.043 1526 Dihedral : 7.182 57.771 1295 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.69 (0.26), residues: 1133 helix: 0.20 (0.22), residues: 610 sheet: -0.10 (0.72), residues: 53 loop : -1.31 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 413 HIS 0.005 0.001 HIS A 141 PHE 0.019 0.002 PHE A 74 TYR 0.018 0.001 TYR A 289 ARG 0.008 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7889 (mt0) cc_final: 0.7438 (tm-30) REVERT: A 243 GLU cc_start: 0.8525 (pp20) cc_final: 0.8315 (pp20) REVERT: A 249 LEU cc_start: 0.9218 (tt) cc_final: 0.8964 (tt) REVERT: A 293 ILE cc_start: 0.9153 (pt) cc_final: 0.8768 (mp) REVERT: A 297 MET cc_start: 0.8662 (mmp) cc_final: 0.8415 (mmm) REVERT: B 122 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6811 (mm-30) REVERT: B 130 ASP cc_start: 0.6103 (m-30) cc_final: 0.5373 (m-30) REVERT: B 203 THR cc_start: 0.8268 (p) cc_final: 0.7996 (t) REVERT: B 243 GLU cc_start: 0.8335 (pp20) cc_final: 0.8083 (pp20) REVERT: B 289 TYR cc_start: 0.7743 (m-80) cc_final: 0.7384 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1592 time to fit residues: 50.5015 Evaluate side-chains 177 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9067 Z= 0.227 Angle : 0.740 11.687 12286 Z= 0.360 Chirality : 0.044 0.250 1469 Planarity : 0.005 0.070 1526 Dihedral : 7.274 56.864 1295 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.67 (0.26), residues: 1133 helix: 0.22 (0.22), residues: 610 sheet: -0.17 (0.72), residues: 53 loop : -1.30 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS B 535 PHE 0.023 0.002 PHE A 74 TYR 0.016 0.001 TYR B 350 ARG 0.005 0.000 ARG B 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8725 (tt) cc_final: 0.8362 (tt) REVERT: A 249 LEU cc_start: 0.9237 (tt) cc_final: 0.8960 (tt) REVERT: A 293 ILE cc_start: 0.9193 (pt) cc_final: 0.8791 (mp) REVERT: A 297 MET cc_start: 0.8732 (mmp) cc_final: 0.8477 (mmm) REVERT: A 311 ILE cc_start: 0.8806 (mm) cc_final: 0.8535 (tp) REVERT: B 203 THR cc_start: 0.8445 (p) cc_final: 0.8067 (t) REVERT: B 243 GLU cc_start: 0.8427 (pp20) cc_final: 0.8148 (pp20) REVERT: B 289 TYR cc_start: 0.7785 (m-80) cc_final: 0.7396 (m-80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1523 time to fit residues: 46.9789 Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 129 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057411 restraints weight = 33675.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060003 restraints weight = 19768.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061817 restraints weight = 13516.866| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9067 Z= 0.240 Angle : 0.747 11.660 12286 Z= 0.365 Chirality : 0.045 0.248 1469 Planarity : 0.004 0.060 1526 Dihedral : 7.292 56.932 1295 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.26), residues: 1133 helix: 0.18 (0.22), residues: 609 sheet: -0.03 (0.67), residues: 63 loop : -1.24 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.004 0.001 HIS B 535 PHE 0.021 0.002 PHE A 74 TYR 0.019 0.001 TYR A 289 ARG 0.006 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1958.20 seconds wall clock time: 36 minutes 33.07 seconds (2193.07 seconds total)