Starting phenix.real_space_refine on Thu Feb 13 18:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ips_35642/02_2025/8ips_35642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ips_35642/02_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_35642/02_2025/8ips_35642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ips_35642/02_2025/8ips_35642.map" model { file = "/net/cci-nas-00/data/ceres_data/8ips_35642/02_2025/8ips_35642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ips_35642/02_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-5592/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: 4.16, per 1000 atoms: 0.46 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: 2.40 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: 1.13 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: 2.87 Time building geometry restraints manager: 2.76 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: 0.000 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.050 Find NCS groups from input model: 0.150 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- 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 : 0.993 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: 0.2513 time to fit residues: 27.4686 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 : 1.025 ------------------------------------------------------------------------------- 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 = 0.110018 restraints weight = 14639.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110965 restraints weight = 12444.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111661 restraints weight = 10961.000| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 1.008 Fit side-chains REVERT: A 528 MET cc_start: 0.8515 (ptt) cc_final: 0.8245 (ptt) REVERT: B 1 MET cc_start: 0.6658 (tmm) cc_final: 0.6004 (pmm) REVERT: B 19 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 129 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8031 (mt0) outliers start: 33 outliers final: 16 residues processed: 98 average time/residue: 0.2260 time to fit residues: 30.7917 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 : 1.021 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.135528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107747 restraints weight = 15003.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107902 restraints weight = 12212.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109009 restraints weight = 10172.916| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1067 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= 0.216 Angle : 0.586 11.245 12588 Z= 0.291 Chirality : 0.038 0.148 1456 Planarity : 0.005 0.052 1608 Dihedral : 5.901 78.909 1277 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 4.35 % Allowed : 29.06 % Favored : 66.60 % 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: 0.61 (0.26), residues: 1157 helix: 2.09 (0.21), residues: 649 sheet: -0.49 (0.68), residues: 58 loop : -2.17 (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 0.016 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.007 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: 41 poor density : 64 time to evaluate : 1.068 Fit side-chains REVERT: A 527 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8184 (tt) REVERT: A 569 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: B 1 MET cc_start: 0.6467 (tmm) cc_final: 0.5843 (pmm) REVERT: B 19 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 129 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: B 225 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7897 (tt) outliers start: 41 outliers final: 24 residues processed: 98 average time/residue: 0.1905 time to fit residues: 27.8805 Evaluate side-chains 90 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 545 MET 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 129 GLN 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 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: 2.9990 chunk 102 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.137093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109838 restraints weight = 14735.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110379 restraints weight = 13509.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111424 restraints weight = 11166.406| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 0.041 9256 Z= 0.182 Angle : 0.554 10.064 12588 Z= 0.275 Chirality : 0.038 0.145 1456 Planarity : 0.004 0.047 1608 Dihedral : 5.853 79.794 1277 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.09 % Rotamer: Outliers : 5.09 % Allowed : 29.37 % Favored : 65.54 % 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: 2.21 (0.21), residues: 649 sheet: -0.47 (0.68), residues: 58 loop : -2.08 (0.27), residues: 450 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 0.014 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 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 67 time to evaluate : 0.941 Fit side-chains REVERT: A 527 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 569 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 1 MET cc_start: 0.6525 (tmm) cc_final: 0.5879 (pmm) REVERT: B 129 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7976 (mt0) outliers start: 48 outliers final: 24 residues processed: 106 average time/residue: 0.1940 time to fit residues: 30.0798 Evaluate side-chains 91 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 569 PHE 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 158 ILE 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 245 LEU 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 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: 3.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 103 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 99 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.139036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112055 restraints weight = 14849.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112033 restraints weight = 14293.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113325 restraints weight = 11443.384| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9256 Z= 0.170 Angle : 0.560 9.551 12588 Z= 0.271 Chirality : 0.038 0.153 1456 Planarity : 0.004 0.048 1608 Dihedral : 5.817 79.208 1277 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.09 % Rotamer: Outliers : 4.14 % Allowed : 30.65 % 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: 0.87 (0.26), residues: 1157 helix: 2.27 (0.21), residues: 654 sheet: -0.40 (0.69), residues: 58 loop : -2.02 (0.27), residues: 445 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 0.013 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.007 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 105 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 66 time to evaluate : 0.924 Fit side-chains REVERT: B 1 MET cc_start: 0.6532 (tmm) cc_final: 0.5909 (pmm) outliers start: 39 outliers final: 23 residues processed: 99 average time/residue: 0.1941 time to fit residues: 28.1766 Evaluate side-chains 86 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 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 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 280 HIS Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 382 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.133533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106940 restraints weight = 14772.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106724 restraints weight = 13337.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107059 restraints weight = 12234.182| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9256 Z= 0.258 Angle : 0.617 13.646 12588 Z= 0.301 Chirality : 0.040 0.142 1456 Planarity : 0.004 0.046 1608 Dihedral : 5.817 75.890 1277 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.17 % Favored : 92.65 % Rotamer: Outliers : 5.51 % Allowed : 30.12 % 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: 0.68 (0.26), residues: 1157 helix: 2.13 (0.21), residues: 651 sheet: -0.64 (0.67), residues: 58 loop : -2.08 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 427 HIS 0.004 0.001 HIS A 85 PHE 0.018 0.001 PHE A 164 TYR 0.017 0.001 TYR A 134 ARG 0.005 0.000 ARG A 115 *********************** 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 116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 64 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6493 (tmm) cc_final: 0.5965 (pmm) outliers start: 52 outliers final: 38 residues processed: 110 average time/residue: 0.2140 time to fit residues: 34.0744 Evaluate side-chains 101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 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 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 286 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.136437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109158 restraints weight = 14889.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109856 restraints weight = 12940.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110566 restraints weight = 10688.225| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1585 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= 0.188 Angle : 0.574 11.304 12588 Z= 0.279 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.046 1608 Dihedral : 5.792 77.874 1277 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.74 % Favored : 93.09 % Rotamer: Outliers : 3.82 % Allowed : 31.39 % 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: 0.83 (0.26), residues: 1157 helix: 2.24 (0.21), residues: 655 sheet: -0.60 (0.67), residues: 58 loop : -2.03 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.004 0.001 HIS B 280 PHE 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.004 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 103 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6533 (tmm) cc_final: 0.6016 (pmm) REVERT: B 185 MET cc_start: 0.7917 (ttp) cc_final: 0.7691 (ttm) outliers start: 36 outliers final: 29 residues processed: 99 average time/residue: 0.2196 time to fit residues: 30.8438 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 : 1.056 ------------------------------------------------------------------------------- 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 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 451 ARG 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 52 MET Chi-restraints excluded: chain B residue 66 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.137463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110279 restraints weight = 15047.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110924 restraints weight = 13030.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111688 restraints weight = 10833.278| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1678 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= 0.181 Angle : 0.575 9.940 12588 Z= 0.279 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.747 78.109 1277 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 3.92 % Allowed : 31.92 % Favored : 64.16 % 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: 0.96 (0.26), residues: 1157 helix: 2.38 (0.21), residues: 649 sheet: -0.19 (0.65), residues: 68 loop : -2.07 (0.27), residues: 440 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 0.014 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 *********************** 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 102 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6509 (tmm) cc_final: 0.6002 (pmm) REVERT: B 185 MET cc_start: 0.7905 (ttp) cc_final: 0.7679 (ttm) outliers start: 37 outliers final: 34 residues processed: 98 average time/residue: 0.2010 time to fit residues: 28.3863 Evaluate side-chains 96 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 51 HIS Chi-restraints excluded: chain B residue 66 PHE 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 212 MET 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 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 500 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.136747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109661 restraints weight = 14784.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110163 restraints weight = 13212.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111752 restraints weight = 11384.772| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1708 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= 0.197 Angle : 0.592 11.028 12588 Z= 0.285 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.748 77.673 1277 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.83 % Favored : 93.00 % Rotamer: Outliers : 4.14 % Allowed : 31.60 % 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: 0.93 (0.26), residues: 1157 helix: 2.31 (0.21), residues: 659 sheet: -0.22 (0.65), residues: 68 loop : -2.10 (0.28), residues: 430 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 0.015 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 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 101 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6508 (tmm) cc_final: 0.6004 (pmm) REVERT: B 185 MET cc_start: 0.7893 (ttp) cc_final: 0.7668 (ttm) outliers start: 39 outliers final: 34 residues processed: 98 average time/residue: 0.2130 time to fit residues: 29.7875 Evaluate side-chains 95 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 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 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 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 500 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 91 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110023 restraints weight = 14977.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110594 restraints weight = 13189.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111471 restraints weight = 11532.732| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1765 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 : 0.584 10.085 12588 Z= 0.283 Chirality : 0.038 0.193 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.737 77.920 1277 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.74 % Favored : 93.09 % Rotamer: Outliers : 3.71 % Allowed : 32.24 % Favored : 64.05 % 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: 0.97 (0.26), residues: 1157 helix: 2.34 (0.21), residues: 659 sheet: -0.17 (0.65), residues: 68 loop : -2.09 (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 0.015 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.006 0.000 ARG A 115 ********************** 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 97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6530 (tmm) cc_final: 0.6013 (pmm) REVERT: B 185 MET cc_start: 0.7842 (ttp) cc_final: 0.7608 (ttm) outliers start: 35 outliers final: 33 residues processed: 95 average time/residue: 0.2154 time to fit residues: 29.0029 Evaluate side-chains 95 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 PHE 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 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 533 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 42 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.137378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110378 restraints weight = 14971.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110721 restraints weight = 13535.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112336 restraints weight = 11543.104| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1805 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= 0.186 Angle : 0.582 9.836 12588 Z= 0.283 Chirality : 0.038 0.174 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.718 78.054 1277 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 3.61 % Allowed : 32.24 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1157 helix: 2.36 (0.21), residues: 660 sheet: -0.17 (0.65), residues: 68 loop : -2.06 (0.28), residues: 429 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 0.015 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.004 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.60 seconds wall clock time: 46 minutes 7.87 seconds (2767.87 seconds total)