Starting phenix.real_space_refine on Sat Dec 28 22:13:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_35642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_35642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_35642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_35642.map" model { file = "/net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_35642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ips_35642/12_2024/8ips_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-5532/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: 6.22, per 1000 atoms: 0.69 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: 2.57 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.55 Time building geometry restraints manager: 2.91 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: 0.010 Normalize map: mean=0, sd=1: 2.370 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.440 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- 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 : 1.009 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: 0.2457 time to fit residues: 26.6849 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 : 0.996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 1.070 Fit side-chains REVERT: A 528 MET cc_start: 0.8386 (ptt) cc_final: 0.8137 (ptt) REVERT: B 1 MET cc_start: 0.6401 (tmm) cc_final: 0.5927 (pmm) REVERT: B 19 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 129 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (mt0) outliers start: 33 outliers final: 16 residues processed: 98 average time/residue: 0.2309 time to fit residues: 31.3696 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 : 1.026 ------------------------------------------------------------------------------- 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 58 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1127 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= 0.178 Angle : 0.560 9.965 12588 Z= 0.279 Chirality : 0.038 0.148 1456 Planarity : 0.005 0.051 1608 Dihedral : 5.869 80.047 1277 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.09 % Rotamer: Outliers : 4.14 % Allowed : 29.59 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1157 helix: 2.18 (0.21), residues: 648 sheet: -0.37 (0.69), residues: 58 loop : -2.09 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.005 0.001 HIS A 531 PHE 0.014 0.001 PHE A 164 TYR 0.015 0.001 TYR A 134 ARG 0.006 0.000 ARG A 473 *********************** 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 106 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.960 Fit side-chains REVERT: A 569 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: B 1 MET cc_start: 0.6264 (tmm) cc_final: 0.5690 (pmm) REVERT: B 19 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 39 outliers final: 19 residues processed: 99 average time/residue: 0.1856 time to fit residues: 27.1028 Evaluate side-chains 84 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 MET 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 158 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 LEU 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 103 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 92 optimal weight: 5.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1386 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= 0.310 Angle : 0.641 14.449 12588 Z= 0.317 Chirality : 0.040 0.146 1456 Planarity : 0.005 0.047 1608 Dihedral : 5.939 76.747 1277 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.88 % Allowed : 29.59 % 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: 0.48 (0.26), residues: 1157 helix: 1.98 (0.21), residues: 651 sheet: -0.72 (0.67), residues: 58 loop : -2.19 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 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 111 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 1.171 Fit side-chains REVERT: B 1 MET cc_start: 0.6211 (tmm) cc_final: 0.5864 (pmm) outliers start: 46 outliers final: 31 residues processed: 104 average time/residue: 0.2213 time to fit residues: 33.4458 Evaluate side-chains 92 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 544 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 86 VAL 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 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 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 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1402 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= 0.204 Angle : 0.594 12.179 12588 Z= 0.290 Chirality : 0.038 0.152 1456 Planarity : 0.004 0.047 1608 Dihedral : 5.927 77.707 1277 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.83 % Favored : 93.00 % Rotamer: Outliers : 4.24 % Allowed : 31.07 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1157 helix: 2.12 (0.21), residues: 653 sheet: -0.68 (0.67), residues: 58 loop : -2.15 (0.27), residues: 446 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 0.017 0.001 TYR A 134 ARG 0.012 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 108 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6170 (tmm) cc_final: 0.5870 (pmm) outliers start: 40 outliers final: 28 residues processed: 103 average time/residue: 0.2014 time to fit residues: 30.3927 Evaluate side-chains 93 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 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 66 PHE 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 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 511 GLU 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 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.0470 chunk 107 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1496 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= 0.185 Angle : 0.569 10.109 12588 Z= 0.279 Chirality : 0.038 0.142 1456 Planarity : 0.004 0.046 1608 Dihedral : 5.830 77.936 1277 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.26 % Favored : 92.57 % Rotamer: Outliers : 4.67 % Allowed : 30.86 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1157 helix: 2.18 (0.21), residues: 658 sheet: -0.63 (0.67), residues: 58 loop : -2.07 (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 0.015 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 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: 44 poor density : 68 time to evaluate : 1.026 Fit side-chains REVERT: B 1 MET cc_start: 0.6174 (tmm) cc_final: 0.5921 (pmm) REVERT: B 402 TYR cc_start: 0.8303 (p90) cc_final: 0.8097 (p90) outliers start: 44 outliers final: 33 residues processed: 106 average time/residue: 0.1933 time to fit residues: 29.9270 Evaluate side-chains 97 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1580 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= 0.226 Angle : 0.596 11.760 12588 Z= 0.290 Chirality : 0.039 0.142 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.842 77.001 1277 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Rotamer: Outliers : 4.56 % Allowed : 30.86 % 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: 0.73 (0.26), residues: 1157 helix: 2.18 (0.21), residues: 653 sheet: -0.68 (0.67), residues: 58 loop : -2.08 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.004 0.001 HIS A 531 PHE 0.016 0.001 PHE A 164 TYR 0.017 0.001 TYR A 134 ARG 0.008 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 110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6163 (tmm) cc_final: 0.5909 (pmm) outliers start: 43 outliers final: 34 residues processed: 104 average time/residue: 0.2121 time to fit residues: 31.3678 Evaluate side-chains 98 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 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 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 201 LEU Chi-restraints excluded: chain B residue 225 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1676 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= 0.183 Angle : 0.581 9.970 12588 Z= 0.282 Chirality : 0.038 0.142 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.795 78.342 1277 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.91 % Rotamer: Outliers : 3.50 % Allowed : 31.92 % 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: 0.86 (0.26), residues: 1157 helix: 2.24 (0.21), residues: 659 sheet: -0.64 (0.67), residues: 58 loop : -2.01 (0.28), residues: 440 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 0.014 0.001 PHE A 164 TYR 0.016 0.001 TYR A 134 ARG 0.002 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 98 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.985 Fit side-chains REVERT: B 1 MET cc_start: 0.6143 (tmm) cc_final: 0.5922 (pmm) outliers start: 33 outliers final: 29 residues processed: 95 average time/residue: 0.2197 time to fit residues: 30.6196 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 : 1.076 ------------------------------------------------------------------------------- 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 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 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 134 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 285 VAL 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 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 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.0010 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1700 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= 0.190 Angle : 0.577 10.117 12588 Z= 0.281 Chirality : 0.038 0.142 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.764 77.844 1277 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.83 % Rotamer: Outliers : 3.71 % Allowed : 31.81 % 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: 0.91 (0.26), residues: 1157 helix: 2.34 (0.21), residues: 653 sheet: -0.65 (0.67), residues: 58 loop : -2.01 (0.27), residues: 446 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 0.015 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 99 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6158 (tmm) cc_final: 0.5926 (pmm) outliers start: 35 outliers final: 32 residues processed: 97 average time/residue: 0.2143 time to fit residues: 29.1906 Evaluate side-chains 93 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL 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 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 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1766 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= 0.203 Angle : 0.597 10.694 12588 Z= 0.290 Chirality : 0.038 0.153 1456 Planarity : 0.004 0.043 1608 Dihedral : 5.777 77.646 1277 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.83 % 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: 0.91 (0.26), residues: 1157 helix: 2.31 (0.21), residues: 659 sheet: -0.67 (0.67), residues: 58 loop : -2.04 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 ********************** 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 : 1.367 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6170 (tmm) cc_final: 0.5939 (pmm) outliers start: 35 outliers final: 32 residues processed: 94 average time/residue: 0.2182 time to fit residues: 29.7085 Evaluate side-chains 94 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 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 158 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 285 VAL 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 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 27 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109329 restraints weight = 14835.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109640 restraints weight = 13225.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110392 restraints weight = 11869.385| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1780 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= 0.196 Angle : 0.587 10.547 12588 Z= 0.285 Chirality : 0.038 0.141 1456 Planarity : 0.004 0.044 1608 Dihedral : 5.765 77.872 1277 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 3.61 % Allowed : 32.13 % 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: 0.92 (0.26), residues: 1157 helix: 2.37 (0.21), residues: 652 sheet: -0.67 (0.67), residues: 58 loop : -2.04 (0.27), residues: 447 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 0.016 0.001 TYR A 134 ARG 0.002 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.95 seconds wall clock time: 33 minutes 23.44 seconds (2003.44 seconds total)