Starting phenix.real_space_refine on Thu Mar 13 21:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_35642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_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/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_35642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_35642.map" model { file = "/net/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_35642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ips_35642/03_2025/8ips_35642.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.77, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 45 helices and 4 sheets defined 62.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 13 removed outlier: 4.067A pdb=" N ARG A 13 " --> pdb=" O LEU A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 15 through 50 removed outlier: 3.532A pdb=" N GLY A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 removed outlier: 3.597A pdb=" N LEU A 54 " --> pdb=" O VAL A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 60 through 104 removed outlier: 4.102A pdb=" N ALA A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) 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 119 through 157 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.651A pdb=" N ALA A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) 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 183 through 210 Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.235A pdb=" N ILE A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 266 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) Processing helix chain 'A' and resid 279 through 292 removed outlier: 3.741A pdb=" N PHE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.702A pdb=" N THR A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.510A pdb=" N THR A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 476 through 491 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 506 through 520 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'B' and resid 2 through 16 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) Processing helix chain 'B' and resid 20 through 54 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.543A pdb=" N LEU B 62 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 110 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) removed outlier: 3.825A pdb=" N GLY B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 120 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 164 through 183 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 189 through 211 removed outlier: 3.674A pdb=" N ARG B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.745A pdb=" N ILE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.039A pdb=" N ILE B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.584A pdb=" N PHE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.774A pdb=" N GLY B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 310 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) Processing helix chain 'B' and resid 310 through 329 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 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 480 through 484 removed outlier: 4.011A pdb=" N ALA B 483 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 491 removed outlier: 3.519A pdb=" N ALA B 491 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 502 removed outlier: 3.537A pdb=" N ALA B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 533 Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'B' and resid 575 through 588 removed outlier: 3.940A pdb=" N ILE B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 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=AA2, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.352A pdb=" N SER A 417 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 498 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 541 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 370 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 542 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN A 553 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 544 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 551 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 5.788A pdb=" N ALA B 352 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG B 407 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP B 354 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER B 405 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 401 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 411 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 425 through 428 removed outlier: 6.226A pdb=" N SER B 426 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP B 510 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 428 " --> pdb=" O ASP B 510 " (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: 7.066A pdb=" N ARG B 378 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N TRP B 554 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 380 " --> pdb=" O TRP B 554 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET B 556 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL B 382 " --> pdb=" O MET B 556 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 553 " --> pdb=" O GLN B 564 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN B 564 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 555 " --> pdb=" O ILE B 562 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1470 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: 2.74 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: 0.00 - 1.75: 12194 1.75 - 3.50: 300 3.50 - 5.25: 70 5.25 - 7.00: 15 7.00 - 8.75: 9 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: 1327 2.76 - 3.29: 8561 3.29 - 3.83: 14359 3.83 - 4.36: 14981 4.36 - 4.90: 27360 Nonbonded interactions: 66588 Sorted by model distance: nonbonded pdb=" OE1 GLN B 129 " pdb=" OG SER B 323 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN A 93 " pdb=" OG SER B 232 " model vdw 2.246 3.120 nonbonded pdb=" OG SER A 427 " pdb=" OD2 ASP B 207 " model vdw 2.263 3.040 nonbonded pdb=" NE2 GLN A 563 " pdb=" O GLY A 564 " model vdw 2.267 3.120 nonbonded pdb=" OD1 ASP B 460 " pdb=" N ASN B 461 " model vdw 2.271 3.120 ... (remaining 66583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.360 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- 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= 0.304 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 to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.956 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: 0.2371 time to fit residues: 25.8980 Evaluate side-chains 63 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 0.0980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110019 restraints weight = 14639.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110823 restraints weight = 12445.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111509 restraints weight = 11150.042| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9256 Z= 0.197 Angle : 0.610 12.595 12588 Z= 0.300 Chirality : 0.039 0.153 1456 Planarity : 0.005 0.058 1608 Dihedral : 5.882 78.993 1277 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.50 % Allowed : 29.59 % Favored : 66.91 % 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: 2.07 (0.21), residues: 643 sheet: -0.43 (0.70), residues: 58 loop : -2.19 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.006 0.001 HIS A 531 PHE 0.017 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.003 0.000 ARG B 485 *********************** 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 101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 2.228 Fit side-chains REVERT: A 528 MET cc_start: 0.8514 (ptt) cc_final: 0.8244 (ptt) REVERT: B 1 MET cc_start: 0.6664 (tmm) cc_final: 0.6005 (pmm) REVERT: B 19 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 129 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8032 (mt0) outliers start: 33 outliers final: 16 residues processed: 98 average time/residue: 0.2666 time to fit residues: 36.6352 Evaluate side-chains 79 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 106 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 173 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 383 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 129 GLN 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 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 77 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.0050 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.136860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109565 restraints weight = 14990.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110462 restraints weight = 13598.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111567 restraints weight = 11020.706| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1053 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= 0.194 Angle : 0.572 10.201 12588 Z= 0.284 Chirality : 0.038 0.145 1456 Planarity : 0.005 0.052 1608 Dihedral : 5.885 79.340 1277 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 4.24 % Allowed : 29.06 % Favored : 66.70 % 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: 0.65 (0.26), residues: 1157 helix: 2.12 (0.21), residues: 649 sheet: -0.43 (0.69), residues: 58 loop : -2.15 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.005 0.001 HIS A 531 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.009 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 105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 1.259 Fit side-chains REVERT: A 527 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 569 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: B 1 MET cc_start: 0.6572 (tmm) cc_final: 0.5918 (pmm) outliers start: 40 outliers final: 22 residues processed: 98 average time/residue: 0.1841 time to fit residues: 26.9519 Evaluate side-chains 85 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 383 LEU 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 A residue 560 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 158 ILE 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 441 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 114 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.136387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109302 restraints weight = 14735.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109547 restraints weight = 13540.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110580 restraints weight = 11758.262| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1242 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= 0.197 Angle : 0.566 10.694 12588 Z= 0.280 Chirality : 0.038 0.146 1456 Planarity : 0.004 0.047 1608 Dihedral : 5.843 79.128 1277 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.48 % Rotamer: Outliers : 5.20 % Allowed : 29.59 % Favored : 65.22 % 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: 0.71 (0.26), residues: 1157 helix: 2.18 (0.21), residues: 649 sheet: -0.45 (0.68), residues: 58 loop : -2.12 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.005 0.001 HIS A 531 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.003 0.000 ARG A 115 *********************** 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 117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 68 time to evaluate : 0.990 Fit side-chains REVERT: A 527 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 569 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: B 1 MET cc_start: 0.6519 (tmm) cc_final: 0.5879 (pmm) outliers start: 49 outliers final: 27 residues processed: 108 average time/residue: 0.2307 time to fit residues: 36.3340 Evaluate side-chains 91 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 173 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL 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 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 66 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 280 HIS Chi-restraints excluded: chain B residue 382 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 107 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.137299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110199 restraints weight = 14787.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110276 restraints weight = 13905.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111727 restraints weight = 11538.964| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1394 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= 0.187 Angle : 0.577 10.412 12588 Z= 0.280 Chirality : 0.038 0.151 1456 Planarity : 0.004 0.046 1608 Dihedral : 5.823 78.119 1277 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 4.45 % Allowed : 30.33 % Favored : 65.22 % 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: 0.81 (0.26), residues: 1157 helix: 2.25 (0.21), residues: 648 sheet: -0.44 (0.69), residues: 58 loop : -2.05 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.004 0.001 HIS A 531 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.002 0.000 ARG A 115 *********************** 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 107 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 0.953 Fit side-chains REVERT: B 1 MET cc_start: 0.6533 (tmm) cc_final: 0.5912 (pmm) outliers start: 42 outliers final: 29 residues processed: 102 average time/residue: 0.1938 time to fit residues: 29.6230 Evaluate side-chains 93 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 214 THR Chi-restraints excluded: chain A residue 270 VAL 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 B residue 66 PHE Chi-restraints excluded: chain B residue 86 VAL 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 225 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 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 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 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102914 restraints weight = 14729.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103500 restraints weight = 12253.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104277 restraints weight = 10470.387| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9256 Z= 0.296 Angle : 0.650 15.153 12588 Z= 0.318 Chirality : 0.041 0.144 1456 Planarity : 0.005 0.043 1608 Dihedral : 5.909 75.883 1277 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.52 % Favored : 92.31 % 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: 0.55 (0.26), residues: 1157 helix: 2.03 (0.21), residues: 650 sheet: -0.73 (0.67), residues: 58 loop : -2.13 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.005 0.001 HIS A 85 PHE 0.020 0.001 PHE A 164 TYR 0.018 0.002 TYR A 134 ARG 0.005 0.000 ARG B 493 *********************** 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 112 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 64 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6504 (tmm) cc_final: 0.5970 (pmm) REVERT: B 129 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: B 185 MET cc_start: 0.7714 (ttp) cc_final: 0.7446 (ttm) outliers start: 48 outliers final: 34 residues processed: 106 average time/residue: 0.2236 time to fit residues: 33.5729 Evaluate side-chains 96 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 92 LEU 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 173 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 129 GLN 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 201 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.134288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107842 restraints weight = 14839.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107313 restraints weight = 13221.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108172 restraints weight = 11722.721| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1601 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= 0.206 Angle : 0.601 12.610 12588 Z= 0.293 Chirality : 0.038 0.147 1456 Planarity : 0.004 0.045 1608 Dihedral : 5.900 77.860 1277 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Rotamer: Outliers : 3.92 % Allowed : 31.60 % 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: 0.71 (0.26), residues: 1157 helix: 2.12 (0.21), residues: 658 sheet: -0.68 (0.67), residues: 58 loop : -2.09 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS B 280 PHE 0.016 0.001 PHE A 164 TYR 0.017 0.001 TYR A 134 ARG 0.011 0.000 ARG A 115 *********************** 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 104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7358 (mmm) cc_final: 0.7101 (mmm) REVERT: B 1 MET cc_start: 0.6615 (tmm) cc_final: 0.6061 (pmm) REVERT: B 129 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: B 185 MET cc_start: 0.7796 (ttp) cc_final: 0.7494 (ttm) outliers start: 37 outliers final: 30 residues processed: 102 average time/residue: 0.1893 time to fit residues: 27.9842 Evaluate side-chains 96 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 270 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 451 ARG 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 B residue 20 SER 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 86 VAL Chi-restraints excluded: chain B residue 129 GLN 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 201 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 280 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 533 LEU 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 110 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107936 restraints weight = 15067.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108207 restraints weight = 13017.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108844 restraints weight = 11254.772| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1662 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= 0.199 Angle : 0.593 11.406 12588 Z= 0.288 Chirality : 0.038 0.142 1456 Planarity : 0.004 0.045 1608 Dihedral : 5.851 78.403 1277 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.83 % Rotamer: Outliers : 3.82 % Allowed : 31.60 % 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: 0.76 (0.26), residues: 1157 helix: 2.17 (0.21), residues: 658 sheet: -0.70 (0.67), residues: 58 loop : -2.06 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.004 0.001 HIS A 531 PHE 0.016 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.004 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 104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6726 (tmm) cc_final: 0.6142 (pmm) REVERT: B 129 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: B 185 MET cc_start: 0.7806 (ttp) cc_final: 0.7557 (ttm) REVERT: B 510 ASP cc_start: 0.7906 (t0) cc_final: 0.7649 (t0) outliers start: 36 outliers final: 30 residues processed: 101 average time/residue: 0.2003 time to fit residues: 29.4066 Evaluate side-chains 97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 130 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 383 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 20 SER 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 86 VAL Chi-restraints excluded: chain B residue 129 GLN 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 280 HIS Chi-restraints excluded: chain B residue 286 THR 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 533 LEU 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 19 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.134622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108300 restraints weight = 14828.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107753 restraints weight = 12538.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108298 restraints weight = 10672.193| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1715 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= 0.215 Angle : 0.601 11.906 12588 Z= 0.292 Chirality : 0.039 0.142 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.838 77.947 1277 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.83 % Favored : 93.00 % Rotamer: Outliers : 3.92 % Allowed : 31.28 % Favored : 64.79 % 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: 0.76 (0.26), residues: 1157 helix: 2.18 (0.21), residues: 659 sheet: -0.81 (0.66), residues: 58 loop : -2.08 (0.27), residues: 440 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 0.016 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.003 0.000 ARG A 115 *********************** 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 102 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6720 (tmm) cc_final: 0.6137 (pmm) REVERT: B 129 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: B 185 MET cc_start: 0.7723 (ttp) cc_final: 0.7473 (ttm) outliers start: 37 outliers final: 33 residues processed: 99 average time/residue: 0.2121 time to fit residues: 30.0413 Evaluate side-chains 97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE 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 383 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 20 SER 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 86 VAL Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 134 HIS 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 280 HIS Chi-restraints excluded: chain B residue 286 THR 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 533 LEU 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 88 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.136408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109153 restraints weight = 14980.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109503 restraints weight = 13348.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110165 restraints weight = 12045.755| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1769 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= 0.187 Angle : 0.588 10.440 12588 Z= 0.286 Chirality : 0.038 0.155 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.808 78.885 1277 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Rotamer: Outliers : 2.97 % Allowed : 32.45 % 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: 0.90 (0.26), residues: 1157 helix: 2.34 (0.21), residues: 653 sheet: -0.75 (0.66), residues: 58 loop : -2.04 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS A 531 PHE 0.014 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.002 0.000 ARG B 485 ********************** 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 92 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6744 (tmm) cc_final: 0.6167 (pmm) REVERT: B 185 MET cc_start: 0.7696 (ttp) cc_final: 0.7465 (ttm) outliers start: 28 outliers final: 25 residues processed: 90 average time/residue: 0.2306 time to fit residues: 30.7622 Evaluate side-chains 89 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 225 ILE 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 533 LEU 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 42 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.0040 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109023 restraints weight = 14988.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109525 restraints weight = 13149.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110244 restraints weight = 11936.224| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1796 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= 0.193 Angle : 0.585 10.493 12588 Z= 0.284 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.782 78.551 1277 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.91 % Rotamer: Outliers : 3.29 % Allowed : 32.13 % 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: 0.90 (0.26), residues: 1157 helix: 2.32 (0.21), residues: 654 sheet: -0.33 (0.65), residues: 68 loop : -2.11 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.003 0.001 HIS A 531 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.98 seconds wall clock time: 48 minutes 53.30 seconds (2933.30 seconds total)