Starting phenix.real_space_refine on Wed Feb 14 10:28:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ips_35642/02_2024/8ips_35642_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.050 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 30 5.16 5 C 5823 2.51 5 N 1591 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" 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: 9071 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "B" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4595 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.61 Number of scatterers: 9071 At special positions: 0 Unit cell: (85.44, 92.16, 144.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 30 16.00 O 1626 8.00 N 1591 7.00 C 5823 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 6 sheets defined 57.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Proline residue: A 6 - end of helix removed outlier: 4.054A pdb=" N LEU A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 49 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 61 through 104 removed outlier: 4.123A pdb=" N GLY A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 89 " --> pdb=" O HIS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 156 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 160 through 181 removed outlier: 3.899A pdb=" N MET A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 184 through 215 removed outlier: 5.356A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 212 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 267 removed outlier: 3.587A pdb=" N LEU A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.820A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 300 through 320 removed outlier: 3.664A pdb=" N LEU A 304 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 305 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 306 " --> pdb=" O HIS A 303 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 477 through 490 removed outlier: 4.126A pdb=" N ARG A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 519 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.747A pdb=" N ALA A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.689A pdb=" N GLN B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 8 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 64 through 109 removed outlier: 4.329A pdb=" N LEU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 121 through 159 removed outlier: 3.942A pdb=" N ASP B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Proline residue: B 142 - end of helix removed outlier: 3.940A pdb=" N VAL B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.841A pdb=" N THR B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 190 through 217 removed outlier: 3.545A pdb=" N MET B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N THR B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.652A pdb=" N ARG B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 287 through 328 Proline residue: B 298 - end of helix removed outlier: 4.105A pdb=" N PHE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.556A pdb=" N LEU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N HIS B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 397 removed outlier: 3.856A pdb=" N LEU B 392 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU B 393 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 424 removed outlier: 4.846A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N HIS B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 567 through 570 No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 576 through 587 Processing sheet with id= A, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.732A pdb=" N LEU A 339 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 342 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU A 396 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 526 through 529 removed outlier: 7.091A pdb=" N GLN A 541 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU A 372 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 543 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 544 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 552 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP A 546 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.857A pdb=" N LEU A 495 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL A 419 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A 497 " --> pdb=" O VAL A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 370 through 373 removed outlier: 3.912A pdb=" N PHE B 371 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 350 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 353 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 405 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.108A pdb=" N SER B 401 " --> pdb=" O THR B 358 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 552 through 556 removed outlier: 3.863A pdb=" N VAL B 552 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR B 537 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 381 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET B 539 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLY B 383 " --> pdb=" O MET B 539 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 507 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 540 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 509 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 426 " --> pdb=" O LEU B 506 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1305 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: 2.61 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3157 1.37 - 1.55: 6038 1.55 - 1.73: 0 1.73 - 1.91: 58 1.91 - 2.09: 3 Bond restraints: 9256 Sorted by residual: bond pdb=" C3C HEM A 601 " pdb=" CAC HEM A 601 " ideal model delta sigma weight residual 1.544 1.450 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C3B HEM A 601 " pdb=" CAB HEM A 601 " ideal model delta sigma weight residual 1.544 1.454 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C ILE B 48 " pdb=" O ILE B 48 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.12e-02 7.97e+03 1.34e+01 bond pdb=" N ILE B 38 " pdb=" CA ILE B 38 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" CA ALA B 42 " pdb=" CB ALA B 42 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.21e+01 ... (remaining 9251 not shown) Histogram of bond angle deviations from ideal: 86.61 - 104.72: 136 104.72 - 122.83: 11736 122.83 - 140.95: 714 140.95 - 159.06: 0 159.06 - 177.17: 2 Bond angle restraints: 12588 Sorted by residual: angle pdb=" CA PHE B 467 " pdb=" CB PHE B 467 " pdb=" CG PHE B 467 " ideal model delta sigma weight residual 113.80 118.89 -5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" C GLN B 50 " pdb=" CA GLN B 50 " pdb=" CB GLN B 50 " ideal model delta sigma weight residual 110.67 102.36 8.31 1.92e+00 2.71e-01 1.87e+01 angle pdb=" C ILE B 36 " pdb=" N LEU B 37 " pdb=" CA LEU B 37 " ideal model delta sigma weight residual 120.29 114.24 6.05 1.42e+00 4.96e-01 1.81e+01 angle pdb=" CA ILE B 48 " pdb=" C ILE B 48 " pdb=" O ILE B 48 " ideal model delta sigma weight residual 121.05 116.37 4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" CA LEU B 37 " pdb=" C LEU B 37 " pdb=" O LEU B 37 " ideal model delta sigma weight residual 120.42 116.42 4.00 1.06e+00 8.90e-01 1.42e+01 ... (remaining 12583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4637 17.97 - 35.94: 645 35.94 - 53.90: 177 53.90 - 71.87: 34 71.87 - 89.84: 16 Dihedral angle restraints: 5509 sinusoidal: 2178 harmonic: 3331 Sorted by residual: dihedral pdb=" C2C HEM A 601 " pdb=" C3C HEM A 601 " pdb=" CAC HEM A 601 " pdb=" CBC HEM A 601 " ideal model delta sinusoidal sigma weight residual -180.00 -100.00 -80.00 2 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" C2B HEM A 601 " pdb=" C3B HEM A 601 " pdb=" CAB HEM A 601 " pdb=" CBB HEM A 601 " ideal model delta sinusoidal sigma weight residual 180.00 114.26 65.74 2 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CA ASP A 461 " pdb=" C ASP A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 908 0.029 - 0.059: 346 0.059 - 0.088: 121 0.088 - 0.117: 68 0.117 - 0.146: 13 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA GLN B 50 " pdb=" N GLN B 50 " pdb=" C GLN B 50 " pdb=" CB GLN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA LEU B 37 " pdb=" N LEU B 37 " pdb=" C LEU B 37 " pdb=" CB LEU B 37 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CG LEU A 120 " pdb=" CB LEU A 120 " pdb=" CD1 LEU A 120 " pdb=" CD2 LEU A 120 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1453 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 173 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 174 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 176 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO B 177 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 36 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ILE B 36 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 36 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 37 " 0.014 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1333 2.76 - 3.29: 8608 3.29 - 3.83: 14396 3.83 - 4.36: 15053 4.36 - 4.90: 27370 Nonbonded interactions: 66760 Sorted by model distance: nonbonded pdb=" OE1 GLN B 129 " pdb=" OG SER B 323 " model vdw 2.221 2.440 nonbonded pdb=" NE2 GLN A 93 " pdb=" OG SER B 232 " model vdw 2.246 2.520 nonbonded pdb=" OG SER A 427 " pdb=" OD2 ASP B 207 " model vdw 2.263 2.440 nonbonded pdb=" NE2 GLN A 563 " pdb=" O GLY A 564 " model vdw 2.267 2.520 nonbonded pdb=" OD1 ASP B 460 " pdb=" N ASN B 461 " model vdw 2.271 2.520 ... (remaining 66755 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 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: 1.320 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: 0.000 Extract box with map and model: 7.180 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.960 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 9256 Z= 0.359 Angle : 0.703 8.754 12588 Z= 0.382 Chirality : 0.040 0.146 1456 Planarity : 0.005 0.073 1608 Dihedral : 18.308 89.837 3361 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.21 % Allowed : 30.01 % Favored : 69.78 % 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: 0.29 (0.26), residues: 1157 helix: 1.79 (0.22), residues: 636 sheet: 0.04 (0.65), residues: 73 loop : -2.28 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 41 HIS 0.003 0.001 HIS A 85 PHE 0.022 0.001 PHE B 467 TYR 0.016 0.001 TYR A 134 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.004 Fit side-chains REVERT: A 149 MET cc_start: 0.7147 (mmm) cc_final: 0.6905 (mmm) outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.2505 time to fit residues: 27.2371 Evaluate side-chains 63 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 488 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9256 Z= 0.275 Angle : 0.641 14.970 12588 Z= 0.313 Chirality : 0.040 0.154 1456 Planarity : 0.005 0.062 1608 Dihedral : 5.945 79.455 1277 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.45 % Allowed : 29.69 % Favored : 65.85 % 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: 0.40 (0.25), residues: 1157 helix: 1.88 (0.22), residues: 633 sheet: -0.20 (0.61), residues: 73 loop : -2.16 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.005 0.001 HIS A 531 PHE 0.019 0.001 PHE A 164 TYR 0.017 0.002 TYR A 134 ARG 0.003 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 65 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 527 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8375 (tt) REVERT: A 528 MET cc_start: 0.8330 (ptt) cc_final: 0.8121 (ptt) REVERT: B 1 MET cc_start: 0.6391 (tmm) cc_final: 0.5899 (pmm) REVERT: B 225 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8002 (tt) outliers start: 42 outliers final: 24 residues processed: 103 average time/residue: 0.2208 time to fit residues: 31.5957 Evaluate side-chains 88 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9256 Z= 0.184 Angle : 0.562 10.499 12588 Z= 0.277 Chirality : 0.038 0.145 1456 Planarity : 0.005 0.052 1608 Dihedral : 5.898 80.574 1277 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.56 % Allowed : 30.01 % Favored : 65.43 % 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: 0.59 (0.26), residues: 1157 helix: 1.96 (0.22), residues: 654 sheet: 0.04 (0.64), residues: 73 loop : -2.16 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.005 0.001 HIS A 531 PHE 0.014 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.008 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 69 time to evaluate : 1.018 Fit side-chains REVERT: A 362 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6038 (tp40) REVERT: A 569 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: B 1 MET cc_start: 0.6227 (tmm) cc_final: 0.5747 (pmm) outliers start: 43 outliers final: 24 residues processed: 104 average time/residue: 0.1844 time to fit residues: 28.2013 Evaluate side-chains 93 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9256 Z= 0.190 Angle : 0.558 11.261 12588 Z= 0.272 Chirality : 0.038 0.145 1456 Planarity : 0.004 0.049 1608 Dihedral : 5.776 77.920 1277 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.09 % Allowed : 30.33 % Favored : 64.58 % 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: 0.67 (0.26), residues: 1157 helix: 2.06 (0.22), residues: 647 sheet: -0.01 (0.64), residues: 73 loop : -2.09 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 427 HIS 0.004 0.001 HIS A 531 PHE 0.016 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.003 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 66 time to evaluate : 1.004 Fit side-chains REVERT: A 569 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: B 1 MET cc_start: 0.6233 (tmm) cc_final: 0.5794 (pmm) REVERT: B 185 MET cc_start: 0.7549 (ttp) cc_final: 0.7287 (ttm) outliers start: 48 outliers final: 32 residues processed: 105 average time/residue: 0.1914 time to fit residues: 29.2214 Evaluate side-chains 94 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 61 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9256 Z= 0.196 Angle : 0.563 11.201 12588 Z= 0.275 Chirality : 0.038 0.153 1456 Planarity : 0.004 0.050 1608 Dihedral : 5.778 78.088 1277 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.73 % Allowed : 30.33 % Favored : 63.94 % 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: 1157 helix: 2.14 (0.22), residues: 641 sheet: -0.40 (0.62), residues: 76 loop : -2.14 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 427 HIS 0.004 0.001 HIS A 531 PHE 0.015 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 65 time to evaluate : 1.033 Fit side-chains REVERT: B 1 MET cc_start: 0.6209 (tmm) cc_final: 0.5721 (pmm) REVERT: B 225 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (tt) outliers start: 54 outliers final: 40 residues processed: 111 average time/residue: 0.1827 time to fit residues: 30.1868 Evaluate side-chains 104 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 63 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9256 Z= 0.178 Angle : 0.547 9.977 12588 Z= 0.267 Chirality : 0.038 0.148 1456 Planarity : 0.004 0.047 1608 Dihedral : 5.719 78.560 1277 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.20 % Allowed : 30.33 % Favored : 64.48 % 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: 0.75 (0.26), residues: 1157 helix: 2.10 (0.22), residues: 654 sheet: -0.11 (0.63), residues: 73 loop : -2.07 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.003 0.001 HIS B 280 PHE 0.014 0.001 PHE A 164 TYR 0.014 0.001 TYR A 134 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 69 time to evaluate : 1.050 Fit side-chains REVERT: A 527 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 1 MET cc_start: 0.6185 (tmm) cc_final: 0.5761 (pmm) REVERT: B 185 MET cc_start: 0.7512 (ttp) cc_final: 0.7282 (ttm) outliers start: 49 outliers final: 37 residues processed: 111 average time/residue: 0.1984 time to fit residues: 32.0799 Evaluate side-chains 104 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 66 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9256 Z= 0.182 Angle : 0.558 10.126 12588 Z= 0.271 Chirality : 0.038 0.145 1456 Planarity : 0.004 0.049 1608 Dihedral : 5.697 78.463 1277 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.62 % Allowed : 30.43 % Favored : 63.94 % 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: 0.75 (0.26), residues: 1157 helix: 2.12 (0.22), residues: 654 sheet: -0.41 (0.62), residues: 76 loop : -2.05 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.001 PHE A 164 TYR 0.014 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 64 time to evaluate : 1.302 Fit side-chains REVERT: A 527 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 1 MET cc_start: 0.6170 (tmm) cc_final: 0.5747 (pmm) REVERT: B 185 MET cc_start: 0.7428 (ttp) cc_final: 0.7177 (ttm) REVERT: B 225 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 263 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8936 (mm) outliers start: 53 outliers final: 42 residues processed: 110 average time/residue: 0.1921 time to fit residues: 30.9415 Evaluate side-chains 107 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 62 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.0070 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9256 Z= 0.176 Angle : 0.553 9.696 12588 Z= 0.270 Chirality : 0.038 0.156 1456 Planarity : 0.004 0.048 1608 Dihedral : 5.677 78.717 1277 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 4.98 % Allowed : 30.54 % Favored : 64.48 % 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: 1157 helix: 2.09 (0.22), residues: 660 sheet: -0.21 (0.59), residues: 81 loop : -2.09 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.001 PHE A 164 TYR 0.014 0.001 TYR A 134 ARG 0.008 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 66 time to evaluate : 0.995 Fit side-chains REVERT: A 527 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 1 MET cc_start: 0.6158 (tmm) cc_final: 0.5749 (pmm) REVERT: B 185 MET cc_start: 0.7464 (ttp) cc_final: 0.7231 (ttm) outliers start: 47 outliers final: 38 residues processed: 109 average time/residue: 0.1865 time to fit residues: 29.7610 Evaluate side-chains 104 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 65 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9256 Z= 0.177 Angle : 0.550 9.651 12588 Z= 0.267 Chirality : 0.038 0.143 1456 Planarity : 0.004 0.048 1608 Dihedral : 5.638 78.420 1277 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.00 % Favored : 92.91 % Rotamer: Outliers : 4.77 % Allowed : 30.86 % Favored : 64.37 % 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: 0.78 (0.26), residues: 1157 helix: 2.24 (0.22), residues: 645 sheet: -0.19 (0.59), residues: 81 loop : -2.19 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.003 0.001 HIS B 280 PHE 0.014 0.001 PHE A 164 TYR 0.014 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 66 time to evaluate : 1.307 Fit side-chains REVERT: A 527 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 1 MET cc_start: 0.6146 (tmm) cc_final: 0.5748 (pmm) REVERT: B 129 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: B 185 MET cc_start: 0.7416 (ttp) cc_final: 0.7160 (ttm) REVERT: B 225 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7931 (tt) REVERT: B 263 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8934 (mm) outliers start: 45 outliers final: 36 residues processed: 107 average time/residue: 0.2112 time to fit residues: 33.6778 Evaluate side-chains 103 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 63 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9256 Z= 0.368 Angle : 0.681 15.734 12588 Z= 0.331 Chirality : 0.042 0.146 1456 Planarity : 0.005 0.048 1608 Dihedral : 5.871 74.971 1277 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.48 % Rotamer: Outliers : 4.35 % Allowed : 31.28 % Favored : 64.37 % 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: 0.29 (0.26), residues: 1157 helix: 1.78 (0.21), residues: 643 sheet: -1.01 (0.63), residues: 66 loop : -2.11 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 427 HIS 0.006 0.001 HIS A 85 PHE 0.021 0.002 PHE A 164 TYR 0.020 0.002 TYR B 136 ARG 0.005 0.000 ARG B 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 68 time to evaluate : 1.032 Fit side-chains REVERT: A 527 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8390 (tt) REVERT: B 1 MET cc_start: 0.6234 (tmm) cc_final: 0.5735 (pmm) REVERT: B 185 MET cc_start: 0.7364 (ttp) cc_final: 0.7129 (ttm) REVERT: B 225 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8101 (tt) REVERT: B 263 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8969 (mm) outliers start: 41 outliers final: 31 residues processed: 105 average time/residue: 0.1995 time to fit residues: 30.0697 Evaluate side-chains 96 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 62 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.0000 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.133952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107634 restraints weight = 14758.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107510 restraints weight = 12421.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108302 restraints weight = 10371.997| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9256 Z= 0.196 Angle : 0.600 12.644 12588 Z= 0.289 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.048 1608 Dihedral : 5.851 79.496 1277 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 3.50 % Allowed : 32.24 % Favored : 64.26 % 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: 0.54 (0.26), residues: 1157 helix: 2.01 (0.22), residues: 642 sheet: -0.57 (0.61), residues: 76 loop : -2.14 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS B 280 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.002 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.72 seconds wall clock time: 35 minutes 1.08 seconds (2101.08 seconds total)