Starting phenix.real_space_refine on Wed Mar 12 10:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.map" model { file = "/net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d9t_30620/03_2025/7d9t_30620.cif" } resolution = 4.1 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4784 2.51 5 N 1279 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7451 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3235 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 7, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 33, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 518 Conformer: "B" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 7, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 33, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 518 bond proxies already assigned to first conformer: 3276 Chain: "B" Number of atoms: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 263 Conformer: "B" Number of residues, atoms: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 263 bond proxies already assigned to first conformer: 4249 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z90': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 residue: pdb=" N GLU A 325 " occ=0.75 ... (3 atoms not shown) pdb=" CB GLU A 325 " occ=0.75 residue: pdb=" N MET A 341 " occ=0.75 ... (3 atoms not shown) pdb=" CB MET A 341 " occ=0.75 Time building chain proxies: 7.53, per 1000 atoms: 1.01 Number of scatterers: 7451 At special positions: 0 Unit cell: (149.435, 71.06, 100.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1353 8.00 N 1279 7.00 C 4784 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=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.7 seconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 48.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.432A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 4.228A pdb=" N LEU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.584A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.642A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.091A pdb=" N GLY A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.679A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 removed outlier: 3.790A pdb=" N ASP A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.762A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.788A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.009A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 4.153A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.923A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.734A pdb=" N ILE B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.580A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.848A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.796A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 359 through 395 removed outlier: 3.759A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 367 " --> pdb=" O TYR B 363 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 409 removed outlier: 3.969A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 439 through 461 Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.170A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.944A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 3.679A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.931A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 524 removed outlier: 4.529A pdb=" N ASN A 479 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 580 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 618 removed outlier: 4.299A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.881A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.484A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.484A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 587 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 469 hydrogen bonds defined for protein. 1343 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: 2.62 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2452 1.34 - 1.46: 1489 1.46 - 1.58: 3597 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7586 Sorted by residual: bond pdb=" CBN Z90 B 701 " pdb=" CBO Z90 B 701 " ideal model delta sigma weight residual 1.405 1.483 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CAX Z90 B 701 " pdb=" CBG Z90 B 701 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CBE Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.449 1.477 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" CBH Z90 B 701 " pdb=" CBM Z90 B 701 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CBB Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.454 1.472 -0.018 2.00e-02 2.50e+03 7.91e-01 ... (remaining 7581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10212 1.79 - 3.58: 151 3.58 - 5.36: 19 5.36 - 7.15: 7 7.15 - 8.94: 1 Bond angle restraints: 10390 Sorted by residual: angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 111.88 108.21 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" N VAL B 239 " pdb=" CA VAL B 239 " pdb=" C VAL B 239 " ideal model delta sigma weight residual 113.16 108.88 4.28 1.49e+00 4.50e-01 8.24e+00 angle pdb=" N LYS A 555 " pdb=" CA LYS A 555 " pdb=" C LYS A 555 " ideal model delta sigma weight residual 111.36 108.32 3.04 1.09e+00 8.42e-01 7.80e+00 ... (remaining 10385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.30: 4404 28.30 - 56.59: 70 56.59 - 84.89: 4 84.89 - 113.18: 1 113.18 - 141.48: 1 Dihedral angle restraints: 4480 sinusoidal: 1348 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CAX Z90 B 701 " pdb=" CAV Z90 B 701 " pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " ideal model delta sinusoidal sigma weight residual 179.41 37.93 141.48 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CA LEU B 338 " pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 844 0.030 - 0.060: 302 0.060 - 0.090: 85 0.090 - 0.120: 59 0.120 - 0.149: 8 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 403 " pdb=" N ILE A 403 " pdb=" C ILE A 403 " pdb=" CB ILE A 403 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1295 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 554 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL A 554 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 554 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 555 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " 0.007 2.00e-02 2.50e+03 8.69e-03 1.32e+00 pdb=" CG PHE B 4 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 458 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 459 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " 0.015 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1366 2.76 - 3.30: 7435 3.30 - 3.83: 12064 3.83 - 4.37: 12847 4.37 - 4.90: 22726 Nonbonded interactions: 56438 Sorted by model distance: nonbonded pdb=" O VAL B 397 " pdb=" OH TYR B 470 " model vdw 2.230 3.040 nonbonded pdb=" NH2 ARG B 238 " pdb=" OD2 ASP B 342 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 454 " pdb=" O GLY B 476 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 223 " pdb=" OG SER B 318 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG B 121 " pdb=" O SER B 270 " model vdw 2.310 3.120 ... (remaining 56433 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=0.30 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: 0.810 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.003 0.078 7586 Z= 0.184 Angle : 0.567 8.938 10390 Z= 0.320 Chirality : 0.039 0.149 1298 Planarity : 0.003 0.026 1334 Dihedral : 11.031 141.481 2442 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.91 (0.25), residues: 1052 helix: -0.27 (0.22), residues: 496 sheet: -1.81 (0.31), residues: 220 loop : -2.18 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 467 HIS 0.001 0.001 HIS B 271 PHE 0.019 0.001 PHE B 4 TYR 0.017 0.001 TYR A 399 ARG 0.001 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8093 (t0) cc_final: 0.7783 (t0) REVERT: A 321 GLU cc_start: 0.7944 (pm20) cc_final: 0.7084 (pm20) REVERT: A 333 GLN cc_start: 0.8954 (pt0) cc_final: 0.8561 (pt0) REVERT: A 455 CYS cc_start: 0.8622 (p) cc_final: 0.8380 (p) REVERT: A 524 LYS cc_start: 0.9199 (tttt) cc_final: 0.8982 (ttmt) REVERT: B 38 LEU cc_start: 0.8927 (tt) cc_final: 0.8496 (mp) REVERT: B 65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8579 (tp30) REVERT: B 69 MET cc_start: 0.8682 (mtp) cc_final: 0.8143 (mtm) REVERT: B 96 GLU cc_start: 0.9008 (mp0) cc_final: 0.8646 (mp0) REVERT: B 406 LEU cc_start: 0.9541 (tp) cc_final: 0.9294 (tt) REVERT: B 473 GLU cc_start: 0.8071 (pp20) cc_final: 0.7822 (tp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1964 time to fit residues: 28.1367 Evaluate side-chains 70 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS B 377 GLN B 548 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050916 restraints weight = 55755.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052831 restraints weight = 28036.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054098 restraints weight = 17576.662| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7586 Z= 0.169 Angle : 0.554 8.031 10390 Z= 0.286 Chirality : 0.041 0.141 1298 Planarity : 0.004 0.041 1334 Dihedral : 6.416 136.219 1137 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1052 helix: 0.69 (0.23), residues: 512 sheet: -1.27 (0.32), residues: 219 loop : -1.77 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 PHE 0.027 0.001 PHE A 162 TYR 0.013 0.001 TYR A 399 ARG 0.007 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9221 (t) cc_final: 0.8552 (p) REVERT: B 65 GLU cc_start: 0.8793 (tp30) cc_final: 0.8453 (tp30) REVERT: B 69 MET cc_start: 0.8693 (mtp) cc_final: 0.8175 (mtm) REVERT: B 96 GLU cc_start: 0.8991 (mp0) cc_final: 0.8744 (mp0) REVERT: B 480 MET cc_start: 0.8917 (ttp) cc_final: 0.8332 (ttp) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.3053 time to fit residues: 38.6772 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.050521 restraints weight = 71550.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.052870 restraints weight = 35327.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054649 restraints weight = 18418.369| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7586 Z= 0.165 Angle : 0.543 8.174 10390 Z= 0.276 Chirality : 0.041 0.153 1298 Planarity : 0.004 0.034 1334 Dihedral : 6.383 136.016 1137 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.19 (0.27), residues: 1052 helix: 1.30 (0.24), residues: 501 sheet: -1.19 (0.32), residues: 228 loop : -1.50 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 PHE 0.020 0.001 PHE A 162 TYR 0.018 0.001 TYR A 399 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 65 GLU cc_start: 0.8816 (tp30) cc_final: 0.8350 (tp30) REVERT: B 69 MET cc_start: 0.8698 (mtp) cc_final: 0.8113 (mtm) REVERT: B 96 GLU cc_start: 0.8979 (mp0) cc_final: 0.8750 (mp0) REVERT: B 473 GLU cc_start: 0.8277 (tp30) cc_final: 0.8015 (tp30) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1387 time to fit residues: 19.3896 Evaluate side-chains 62 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 49 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.051992 restraints weight = 56853.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053982 restraints weight = 26564.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055682 restraints weight = 15502.032| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7586 Z= 0.149 Angle : 0.551 8.477 10390 Z= 0.278 Chirality : 0.041 0.142 1298 Planarity : 0.004 0.034 1334 Dihedral : 6.376 134.631 1137 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.06 (0.27), residues: 1052 helix: 1.48 (0.24), residues: 501 sheet: -0.97 (0.32), residues: 228 loop : -1.42 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.003 0.001 HIS B 437 PHE 0.027 0.001 PHE A 162 TYR 0.014 0.001 TYR A 399 ARG 0.005 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9456 (tpp) cc_final: 0.9223 (tpp) REVERT: B 65 GLU cc_start: 0.8793 (tp30) cc_final: 0.8415 (tp30) REVERT: B 69 MET cc_start: 0.8683 (mtp) cc_final: 0.8120 (mtm) REVERT: B 96 GLU cc_start: 0.8975 (mp0) cc_final: 0.8651 (mp0) REVERT: B 473 GLU cc_start: 0.8236 (tp30) cc_final: 0.8010 (tp30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1735 time to fit residues: 22.0569 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049941 restraints weight = 84336.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052150 restraints weight = 36038.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053649 restraints weight = 20963.774| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7586 Z= 0.177 Angle : 0.547 8.735 10390 Z= 0.278 Chirality : 0.041 0.145 1298 Planarity : 0.004 0.036 1334 Dihedral : 6.416 135.623 1137 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.35 (0.27), residues: 1052 helix: 1.69 (0.24), residues: 504 sheet: -0.78 (0.33), residues: 226 loop : -1.28 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 PHE 0.039 0.002 PHE A 162 TYR 0.020 0.001 TYR A 399 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9426 (tpp) cc_final: 0.9222 (tpp) REVERT: B 65 GLU cc_start: 0.8835 (tp30) cc_final: 0.8469 (tp30) REVERT: B 69 MET cc_start: 0.8699 (mtp) cc_final: 0.8186 (mtm) REVERT: B 96 GLU cc_start: 0.8988 (mp0) cc_final: 0.8674 (mp0) REVERT: B 473 GLU cc_start: 0.8300 (tp30) cc_final: 0.8038 (tp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1455 time to fit residues: 18.1782 Evaluate side-chains 62 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.061388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.050015 restraints weight = 70728.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.052355 restraints weight = 35528.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054150 restraints weight = 18671.234| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7586 Z= 0.191 Angle : 0.551 9.156 10390 Z= 0.280 Chirality : 0.041 0.162 1298 Planarity : 0.004 0.032 1334 Dihedral : 6.499 136.590 1137 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1052 helix: 1.82 (0.24), residues: 504 sheet: -0.66 (0.34), residues: 226 loop : -1.16 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.004 0.001 HIS B 437 PHE 0.030 0.002 PHE A 162 TYR 0.022 0.001 TYR A 399 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9387 (tpp) cc_final: 0.9162 (tpp) REVERT: B 96 GLU cc_start: 0.8952 (mp0) cc_final: 0.8670 (mp0) REVERT: B 473 GLU cc_start: 0.8311 (tp30) cc_final: 0.8022 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1412 time to fit residues: 17.6418 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 2 optimal weight: 5.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.062100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051587 restraints weight = 48456.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053389 restraints weight = 25628.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054665 restraints weight = 16433.596| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.159 Angle : 0.546 9.320 10390 Z= 0.275 Chirality : 0.041 0.167 1298 Planarity : 0.003 0.027 1334 Dihedral : 6.486 136.032 1137 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1052 helix: 1.98 (0.24), residues: 496 sheet: -0.62 (0.34), residues: 226 loop : -1.07 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 PHE 0.027 0.001 PHE A 162 TYR 0.017 0.001 TYR A 399 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9419 (tpp) cc_final: 0.9213 (tpp) REVERT: B 69 MET cc_start: 0.8684 (mtp) cc_final: 0.8480 (mtp) REVERT: B 96 GLU cc_start: 0.8954 (mp0) cc_final: 0.8639 (mp0) REVERT: B 473 GLU cc_start: 0.8311 (tp30) cc_final: 0.8058 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1339 time to fit residues: 16.7246 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.050667 restraints weight = 75434.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053273 restraints weight = 37651.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055034 restraints weight = 18552.413| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.156 Angle : 0.551 9.536 10390 Z= 0.276 Chirality : 0.041 0.156 1298 Planarity : 0.003 0.026 1334 Dihedral : 6.506 135.634 1137 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.74 (0.27), residues: 1052 helix: 2.03 (0.24), residues: 490 sheet: -0.53 (0.34), residues: 226 loop : -1.05 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.003 0.000 HIS B 437 PHE 0.040 0.002 PHE A 162 TYR 0.017 0.001 TYR A 399 ARG 0.002 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9402 (tpp) cc_final: 0.9197 (tpp) REVERT: B 65 GLU cc_start: 0.8700 (tp30) cc_final: 0.8355 (tp30) REVERT: B 69 MET cc_start: 0.8708 (mtp) cc_final: 0.8115 (mtm) REVERT: B 96 GLU cc_start: 0.8987 (mp0) cc_final: 0.8661 (mp0) REVERT: B 473 GLU cc_start: 0.8301 (tp30) cc_final: 0.8069 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1350 time to fit residues: 16.9318 Evaluate side-chains 61 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.062628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051298 restraints weight = 70280.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053819 restraints weight = 35035.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055603 restraints weight = 17789.414| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.159 Angle : 0.562 9.266 10390 Z= 0.284 Chirality : 0.041 0.156 1298 Planarity : 0.003 0.025 1334 Dihedral : 6.519 135.940 1137 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1052 helix: 1.90 (0.24), residues: 497 sheet: -0.53 (0.34), residues: 226 loop : -0.97 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 PHE 0.037 0.002 PHE A 162 TYR 0.017 0.001 TYR A 399 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9391 (tpp) cc_final: 0.9181 (tpp) REVERT: A 465 GLN cc_start: 0.9068 (mp10) cc_final: 0.8676 (mp10) REVERT: B 65 GLU cc_start: 0.8676 (tp30) cc_final: 0.8351 (tp30) REVERT: B 69 MET cc_start: 0.8695 (mtp) cc_final: 0.8097 (mtm) REVERT: B 96 GLU cc_start: 0.8951 (mp0) cc_final: 0.8665 (mp0) REVERT: B 473 GLU cc_start: 0.8287 (tp30) cc_final: 0.8043 (tp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1348 time to fit residues: 16.7273 Evaluate side-chains 66 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 0.0470 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 98 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.063693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.051682 restraints weight = 83172.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053967 restraints weight = 35511.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055455 restraints weight = 20609.812| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7586 Z= 0.144 Angle : 0.545 9.805 10390 Z= 0.273 Chirality : 0.041 0.150 1298 Planarity : 0.003 0.027 1334 Dihedral : 6.496 134.475 1137 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 1052 helix: 2.00 (0.24), residues: 499 sheet: -0.48 (0.34), residues: 226 loop : -0.92 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.002 0.000 HIS B 437 PHE 0.036 0.002 PHE A 162 TYR 0.022 0.001 TYR A 399 ARG 0.002 0.000 ARG B 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9409 (tpp) cc_final: 0.9190 (tpp) REVERT: B 65 GLU cc_start: 0.8701 (tp30) cc_final: 0.8419 (tp30) REVERT: B 69 MET cc_start: 0.8700 (mtp) cc_final: 0.8166 (mtm) REVERT: B 96 GLU cc_start: 0.8970 (mp0) cc_final: 0.8686 (mp0) REVERT: B 473 GLU cc_start: 0.8279 (tp30) cc_final: 0.8066 (tp30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1659 time to fit residues: 21.5647 Evaluate side-chains 64 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 0.0770 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.063386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053236 restraints weight = 43611.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054962 restraints weight = 23880.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.056133 restraints weight = 15577.370| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.167 Angle : 0.571 10.658 10390 Z= 0.286 Chirality : 0.041 0.207 1298 Planarity : 0.004 0.031 1334 Dihedral : 6.580 135.428 1137 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1052 helix: 2.04 (0.24), residues: 499 sheet: -0.43 (0.34), residues: 226 loop : -0.90 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 PHE 0.035 0.002 PHE A 162 TYR 0.014 0.001 TYR A 399 ARG 0.008 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.46 seconds wall clock time: 46 minutes 37.62 seconds (2797.62 seconds total)