Starting phenix.real_space_refine on Wed Sep 17 09:35:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d9t_30620/09_2025/7d9t_30620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d9t_30620/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d9t_30620/09_2025/7d9t_30620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d9t_30620/09_2025/7d9t_30620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d9t_30620/09_2025/7d9t_30620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d9t_30620/09_2025/7d9t_30620.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TYR:plan': 7, 'HIS:plan': 9, 'GLU:plan': 33, 'PHE:plan': 14, 'ARG:plan': 17, 'ASN:plan1': 7, 'GLN:plan1': 12, 'ASP:plan': 18} 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: {'TYR:plan': 7, 'HIS:plan': 9, 'GLU:plan': 33, 'PHE:plan': 14, 'ARG:plan': 17, 'ASN:plan1': 7, 'GLN:plan1': 12, 'ASP:plan': 18} 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: {'GLU:plan': 29, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 10, 'PHE:plan': 2, 'HIS:plan': 2} 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: {'GLU:plan': 29, 'TYR:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 10, 'PHE:plan': 2, 'HIS:plan': 2} 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: 3.31, per 1000 atoms: 0.44 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: 0.74 Conformation dependent library (CDL) restraints added in 565.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.22 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: 1.35 Time building geometry restraints manager: 0.96 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: 0.920 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.430 Find NCS groups from input model: 0.070 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:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- 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= 0.146 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 207 TYR 0.017 0.001 TYR A 399 PHE 0.019 0.001 PHE B 4 TRP 0.004 0.001 TRP A 467 HIS 0.001 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7586) covalent geometry : angle 0.56680 (10390) hydrogen bonds : bond 0.17201 ( 457) hydrogen bonds : angle 6.62449 ( 1343) *********************** 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 : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8093 (t0) cc_final: 0.7782 (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: 0.8983 (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: 0.8578 (tp30) REVERT: B 69 MET cc_start: 0.8682 (mtp) cc_final: 0.8144 (mtm) REVERT: B 96 GLU cc_start: 0.9008 (mp0) cc_final: 0.8645 (mp0) REVERT: B 406 LEU cc_start: 0.9541 (tp) cc_final: 0.9296 (tt) REVERT: B 473 GLU cc_start: 0.8071 (pp20) cc_final: 0.7823 (tp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0901 time to fit residues: 12.7382 Evaluate side-chains 71 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 548 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.060439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.050315 restraints weight = 42977.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.051920 restraints weight = 23638.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053052 restraints weight = 15662.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053817 restraints weight = 11535.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054220 restraints weight = 9197.561| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7586 Z= 0.156 Angle : 0.573 8.212 10390 Z= 0.297 Chirality : 0.041 0.139 1298 Planarity : 0.004 0.041 1334 Dihedral : 6.531 139.124 1137 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.26), residues: 1052 helix: 0.73 (0.23), residues: 513 sheet: -1.42 (0.33), residues: 213 loop : -1.77 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 306 TYR 0.015 0.002 TYR A 399 PHE 0.024 0.002 PHE A 162 TRP 0.006 0.001 TRP B 602 HIS 0.006 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7586) covalent geometry : angle 0.57263 (10390) hydrogen bonds : bond 0.03977 ( 457) hydrogen bonds : angle 4.84246 ( 1343) *********************** 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 83 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9249 (t) cc_final: 0.8591 (p) REVERT: B 69 MET cc_start: 0.8694 (mtp) cc_final: 0.8114 (mtm) REVERT: B 96 GLU cc_start: 0.8985 (mp0) cc_final: 0.8721 (mp0) REVERT: B 480 MET cc_start: 0.8922 (ttp) cc_final: 0.8223 (ttp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0654 time to fit residues: 8.1472 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 4.9990 chunk 86 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 overall best weight: 0.7534 ------------------------------------------------------------------------------- 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 7 HIS B 377 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051013 restraints weight = 42427.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052689 restraints weight = 23044.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.053795 restraints weight = 15047.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.054708 restraints weight = 11125.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055008 restraints weight = 8665.238| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-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: 0.8213 moved from start: 0.1622 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= 0.110 Angle : 0.552 8.123 10390 Z= 0.282 Chirality : 0.041 0.159 1298 Planarity : 0.004 0.038 1334 Dihedral : 6.475 136.733 1137 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.27), residues: 1052 helix: 1.20 (0.24), residues: 507 sheet: -1.31 (0.33), residues: 222 loop : -1.45 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 349 TYR 0.019 0.001 TYR A 399 PHE 0.020 0.001 PHE A 162 TRP 0.006 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7586) covalent geometry : angle 0.55180 (10390) hydrogen bonds : bond 0.03426 ( 457) hydrogen bonds : angle 4.48874 ( 1343) *********************** 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 86 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9224 (t) cc_final: 0.8523 (p) REVERT: A 339 MET cc_start: 0.9468 (tpp) cc_final: 0.9248 (tpp) REVERT: B 65 GLU cc_start: 0.8751 (tp30) cc_final: 0.8366 (tp30) REVERT: B 69 MET cc_start: 0.8661 (mtp) cc_final: 0.8091 (mtm) REVERT: B 96 GLU cc_start: 0.8986 (mp0) cc_final: 0.8716 (mp0) REVERT: B 473 GLU cc_start: 0.8286 (tp30) cc_final: 0.8010 (tp30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0684 time to fit residues: 8.6924 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.060767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.049545 restraints weight = 70617.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.052020 restraints weight = 34159.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053756 restraints weight = 17416.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054342 restraints weight = 11081.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054533 restraints weight = 9349.384| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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: 0.8231 moved from start: 0.1847 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= 0.122 Angle : 0.544 8.411 10390 Z= 0.279 Chirality : 0.041 0.147 1298 Planarity : 0.004 0.032 1334 Dihedral : 6.514 137.263 1137 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.27), residues: 1052 helix: 1.44 (0.24), residues: 509 sheet: -1.07 (0.33), residues: 223 loop : -1.30 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.015 0.001 TYR B 339 PHE 0.015 0.001 PHE A 162 TRP 0.004 0.001 TRP B 22 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7586) covalent geometry : angle 0.54446 (10390) hydrogen bonds : bond 0.03247 ( 457) hydrogen bonds : angle 4.26039 ( 1343) *********************** 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 78 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9201 (t) cc_final: 0.8558 (p) REVERT: A 339 MET cc_start: 0.9414 (tpp) cc_final: 0.9206 (tpp) REVERT: B 65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8411 (tp30) REVERT: B 69 MET cc_start: 0.8676 (mtp) cc_final: 0.8162 (mtm) REVERT: B 473 GLU cc_start: 0.8255 (tp30) cc_final: 0.7983 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0595 time to fit residues: 7.2666 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 0.0060 chunk 50 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 overall best weight: 0.5294 ------------------------------------------------------------------------------- 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** A 600 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 = 0.3136 r_free = 0.3136 target = 0.062001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051172 restraints weight = 56593.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053110 restraints weight = 27510.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054440 restraints weight = 16965.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055425 restraints weight = 11942.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.056166 restraints weight = 9154.769| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 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 = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 7586 Z= 0.103 Angle : 0.551 8.549 10390 Z= 0.277 Chirality : 0.041 0.143 1298 Planarity : 0.004 0.028 1334 Dihedral : 6.505 135.787 1137 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 1052 helix: 1.68 (0.24), residues: 497 sheet: -0.89 (0.33), residues: 228 loop : -1.28 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.041 0.001 TYR A 399 PHE 0.026 0.001 PHE A 162 TRP 0.005 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7586) covalent geometry : angle 0.55052 (10390) hydrogen bonds : bond 0.03115 ( 457) hydrogen bonds : angle 4.11243 ( 1343) *********************** 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 85 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9429 (tpp) cc_final: 0.9195 (tpp) REVERT: A 438 GLN cc_start: 0.8443 (pp30) cc_final: 0.8066 (pp30) REVERT: B 65 GLU cc_start: 0.8729 (tp30) cc_final: 0.8430 (tp30) REVERT: B 69 MET cc_start: 0.8658 (mtp) cc_final: 0.8148 (mtm) REVERT: B 473 GLU cc_start: 0.8278 (tp30) cc_final: 0.8012 (tp30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0569 time to fit residues: 7.5702 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.061197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.050483 restraints weight = 55859.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052260 restraints weight = 28046.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053578 restraints weight = 17860.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054485 restraints weight = 12551.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055232 restraints weight = 9676.124| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 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 = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7586 Z= 0.138 Angle : 0.583 9.763 10390 Z= 0.296 Chirality : 0.041 0.147 1298 Planarity : 0.004 0.041 1334 Dihedral : 6.581 138.233 1137 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.27), residues: 1052 helix: 1.76 (0.24), residues: 502 sheet: -0.76 (0.34), residues: 226 loop : -1.14 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.051 0.002 TYR A 399 PHE 0.031 0.002 PHE B 4 TRP 0.004 0.001 TRP B 22 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7586) covalent geometry : angle 0.58277 (10390) hydrogen bonds : bond 0.03263 ( 457) hydrogen bonds : angle 4.10725 ( 1343) *********************** 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 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9171 (t) cc_final: 0.8581 (p) REVERT: A 339 MET cc_start: 0.9432 (tpp) cc_final: 0.9224 (tpp) REVERT: A 441 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8674 (tm-30) REVERT: B 96 GLU cc_start: 0.8943 (pm20) cc_final: 0.8372 (pm20) REVERT: B 473 GLU cc_start: 0.8303 (tp30) cc_final: 0.7990 (tp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0559 time to fit residues: 7.2458 Evaluate side-chains 63 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.061405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.050082 restraints weight = 83070.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.052579 restraints weight = 39520.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054285 restraints weight = 19165.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055565 restraints weight = 12242.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.055738 restraints weight = 9781.078| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 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 = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2291 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= 0.116 Angle : 0.556 9.263 10390 Z= 0.281 Chirality : 0.042 0.180 1298 Planarity : 0.004 0.030 1334 Dihedral : 6.580 137.662 1137 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.27), residues: 1052 helix: 1.77 (0.24), residues: 504 sheet: -0.69 (0.34), residues: 226 loop : -1.09 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.030 0.001 TYR A 399 PHE 0.018 0.001 PHE B 424 TRP 0.004 0.001 TRP B 602 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7586) covalent geometry : angle 0.55638 (10390) hydrogen bonds : bond 0.03139 ( 457) hydrogen bonds : angle 4.04607 ( 1343) *********************** 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 81 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9148 (t) cc_final: 0.8567 (p) REVERT: A 438 GLN cc_start: 0.8315 (pp30) cc_final: 0.7952 (pp30) REVERT: B 96 GLU cc_start: 0.8914 (pm20) cc_final: 0.8272 (pm20) REVERT: B 473 GLU cc_start: 0.8271 (tp30) cc_final: 0.8008 (tp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0513 time to fit residues: 6.6563 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 overall best weight: 1.0324 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.061403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.050693 restraints weight = 54849.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.052572 restraints weight = 27235.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.053902 restraints weight = 16967.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054754 restraints weight = 11851.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055495 restraints weight = 9219.366| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2372 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= 0.119 Angle : 0.570 10.118 10390 Z= 0.288 Chirality : 0.042 0.182 1298 Planarity : 0.004 0.032 1334 Dihedral : 6.625 138.338 1137 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.27), residues: 1052 helix: 1.75 (0.24), residues: 508 sheet: -0.65 (0.35), residues: 226 loop : -1.01 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.056 0.002 TYR A 399 PHE 0.020 0.001 PHE B 4 TRP 0.004 0.001 TRP B 22 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7586) covalent geometry : angle 0.57050 (10390) hydrogen bonds : bond 0.03186 ( 457) hydrogen bonds : angle 4.03469 ( 1343) *********************** 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 78 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9174 (t) cc_final: 0.8583 (p) REVERT: A 339 MET cc_start: 0.9393 (tpp) cc_final: 0.9044 (tpp) REVERT: A 441 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8659 (tm-30) REVERT: B 96 GLU cc_start: 0.8912 (pm20) cc_final: 0.8500 (pm20) REVERT: B 473 GLU cc_start: 0.8274 (tp30) cc_final: 0.7995 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0532 time to fit residues: 6.5906 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 0.0010 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.061797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.050623 restraints weight = 70847.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053054 restraints weight = 34413.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054761 restraints weight = 17616.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.055804 restraints weight = 11271.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.055896 restraints weight = 8528.791| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2465 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= 0.109 Angle : 0.566 9.552 10390 Z= 0.284 Chirality : 0.041 0.173 1298 Planarity : 0.003 0.029 1334 Dihedral : 6.609 137.215 1137 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 1052 helix: 1.83 (0.24), residues: 502 sheet: -0.59 (0.34), residues: 226 loop : -1.00 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.047 0.002 TYR A 399 PHE 0.021 0.001 PHE B 4 TRP 0.005 0.001 TRP B 22 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7586) covalent geometry : angle 0.56618 (10390) hydrogen bonds : bond 0.03086 ( 457) hydrogen bonds : angle 3.96160 ( 1343) *********************** 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 78 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9127 (t) cc_final: 0.8550 (p) REVERT: A 441 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 96 GLU cc_start: 0.8860 (pm20) cc_final: 0.8461 (pm20) REVERT: B 473 GLU cc_start: 0.8255 (tp30) cc_final: 0.7983 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0578 time to fit residues: 7.1570 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.062539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050441 restraints weight = 97211.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.053463 restraints weight = 43594.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055439 restraints weight = 19829.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.056603 restraints weight = 12133.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056930 restraints weight = 9038.869| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 7586 Z= 0.099 Angle : 0.554 10.368 10390 Z= 0.277 Chirality : 0.041 0.165 1298 Planarity : 0.003 0.029 1334 Dihedral : 6.626 137.005 1137 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.24 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.27), residues: 1052 helix: 1.95 (0.24), residues: 496 sheet: -0.56 (0.34), residues: 226 loop : -0.96 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.027 0.001 TYR A 399 PHE 0.022 0.001 PHE B 4 TRP 0.004 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7586) covalent geometry : angle 0.55380 (10390) hydrogen bonds : bond 0.03000 ( 457) hydrogen bonds : angle 3.89826 ( 1343) ********************** 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 80 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9117 (t) cc_final: 0.8557 (p) REVERT: B 96 GLU cc_start: 0.8904 (pm20) cc_final: 0.8526 (pm20) REVERT: B 473 GLU cc_start: 0.8276 (tp30) cc_final: 0.7977 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0569 time to fit residues: 7.2925 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.062259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049990 restraints weight = 97822.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.052315 restraints weight = 39239.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053957 restraints weight = 22041.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055161 restraints weight = 14577.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.055893 restraints weight = 10582.795| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2641 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= 0.107 Angle : 0.556 10.086 10390 Z= 0.280 Chirality : 0.041 0.168 1298 Planarity : 0.004 0.028 1334 Dihedral : 6.658 137.327 1137 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.14 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.28), residues: 1052 helix: 2.01 (0.24), residues: 498 sheet: -0.49 (0.34), residues: 226 loop : -0.91 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.022 0.001 TYR A 399 PHE 0.019 0.001 PHE B 4 TRP 0.003 0.001 TRP B 602 HIS 0.003 0.000 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7586) covalent geometry : angle 0.55593 (10390) hydrogen bonds : bond 0.03029 ( 457) hydrogen bonds : angle 3.90225 ( 1343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.74 seconds wall clock time: 20 minutes 55.11 seconds (1255.11 seconds total)