Starting phenix.real_space_refine on Wed Sep 17 11:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuz_60916/09_2025/9iuz_60916.cif" } resolution = 3.19 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= 0.022 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 65 5.16 5 C 5286 2.51 5 N 1443 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 8349 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4171 Classifications: {'peptide': 537} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 514} Chain breaks: 4 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 384 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.25 Number of scatterers: 8349 At special positions: 0 Unit cell: (73.95, 120.7, 119, 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 65 16.00 O 1555 8.00 N 1443 7.00 C 5286 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 327.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 46.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 55 through 77 removed outlier: 3.566A pdb=" N GLN B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.649A pdb=" N ILE B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 223 through 247 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 411 through 458 removed outlier: 4.099A pdb=" N ARG B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.567A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.512A pdb=" N GLY B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.568A pdb=" N GLU B 560 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 600 through 621 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.626A pdb=" N MET A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.557A pdb=" N SER A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 457 removed outlier: 3.714A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.510A pdb=" N ILE A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.840A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 533' Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'C' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 114 removed outlier: 4.007A pdb=" N TYR B 133 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 122 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 133 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET B 120 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.670A pdb=" N TYR B 303 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 284 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 275 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU B 289 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 273 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET B 394 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B 379 " --> pdb=" O MET B 394 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 396 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 377 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 398 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 486 through 491 removed outlier: 3.742A pdb=" N PHE B 481 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 478 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 549 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 539 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.513A pdb=" N TYR A 133 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET A 120 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 206 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 192 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.626A pdb=" N TYR A 303 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 491 removed outlier: 3.602A pdb=" N GLY A 478 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 554 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 451 hydrogen bonds defined for protein. 1245 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: 1.21 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1957 1.33 - 1.45: 1713 1.45 - 1.57: 4736 1.57 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 8513 Sorted by residual: bond pdb=" N ILE B 499 " pdb=" CA ILE B 499 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.21e-02 6.83e+03 5.81e+00 bond pdb=" CAC O6E B1001 " pdb=" CAH O6E B1001 " ideal model delta sigma weight residual 1.522 1.561 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" N LEU B 87 " pdb=" CA LEU B 87 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.51e+00 bond pdb=" N MET B 439 " pdb=" CA MET B 439 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.18e+00 bond pdb=" N MET B 431 " pdb=" CA MET B 431 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.75e+00 ... (remaining 8508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11390 2.25 - 4.51: 113 4.51 - 6.76: 10 6.76 - 9.01: 3 9.01 - 11.27: 2 Bond angle restraints: 11518 Sorted by residual: angle pdb=" CAH O6E B1001 " pdb=" CAC O6E B1001 " pdb=" CBJ O6E B1001 " ideal model delta sigma weight residual 112.38 101.11 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C GLN B 498 " pdb=" N ILE B 499 " pdb=" CA ILE B 499 " ideal model delta sigma weight residual 120.42 115.98 4.44 1.42e+00 4.96e-01 9.76e+00 angle pdb=" N LYS A 546 " pdb=" CA LYS A 546 " pdb=" C LYS A 546 " ideal model delta sigma weight residual 114.75 110.83 3.92 1.26e+00 6.30e-01 9.70e+00 angle pdb=" CB MET B 422 " pdb=" CG MET B 422 " pdb=" SD MET B 422 " ideal model delta sigma weight residual 112.70 121.85 -9.15 3.00e+00 1.11e-01 9.31e+00 angle pdb=" C ASN B 430 " pdb=" N MET B 431 " pdb=" CA MET B 431 " ideal model delta sigma weight residual 120.44 116.56 3.88 1.30e+00 5.92e-01 8.93e+00 ... (remaining 11513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4360 18.00 - 36.00: 604 36.00 - 53.99: 163 53.99 - 71.99: 27 71.99 - 89.99: 16 Dihedral angle restraints: 5170 sinusoidal: 2104 harmonic: 3066 Sorted by residual: dihedral pdb=" CA LEU A 550 " pdb=" C LEU A 550 " pdb=" N PHE A 551 " pdb=" CA PHE A 551 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 -87.38 87.38 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 504 " pdb=" CG GLU A 504 " pdb=" CD GLU A 504 " pdb=" OE1 GLU A 504 " ideal model delta sinusoidal sigma weight residual 0.00 -87.30 87.30 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 942 0.037 - 0.075: 248 0.075 - 0.112: 79 0.112 - 0.150: 20 0.150 - 0.187: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CG LEU A 507 " pdb=" CB LEU A 507 " pdb=" CD1 LEU A 507 " pdb=" CD2 LEU A 507 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ASP A 209 " pdb=" N ASP A 209 " pdb=" C ASP A 209 " pdb=" CB ASP A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1287 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 580 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO A 581 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 505 " 0.014 2.00e-02 2.50e+03 1.44e-02 5.18e+00 pdb=" CG TRP A 505 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 505 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 505 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 505 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 505 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 505 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 505 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 505 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 505 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 580 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 581 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1306 2.76 - 3.30: 7834 3.30 - 3.83: 13394 3.83 - 4.37: 14410 4.37 - 4.90: 26089 Nonbonded interactions: 63033 Sorted by model distance: nonbonded pdb=" O VAL A 264 " pdb=" OG1 THR A 268 " model vdw 2.226 3.040 nonbonded pdb=" O ASP B 82 " pdb=" OG SER B 86 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 45 " pdb=" OD2 ASP C 48 " model vdw 2.256 3.040 nonbonded pdb=" O LEU A 614 " pdb=" OG SER A 617 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 495 " pdb=" OE1 GLN A 498 " model vdw 2.259 3.040 ... (remaining 63028 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 111 through 144 or resid 156 through 565 or resid 577 thro \ ugh 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 : 0.002 0.039 8515 Z= 0.125 Angle : 0.562 11.268 11518 Z= 0.297 Chirality : 0.039 0.187 1290 Planarity : 0.004 0.060 1477 Dihedral : 18.043 89.989 3186 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.55 % Allowed : 30.60 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.40 (0.27), residues: 1039 helix: 2.89 (0.25), residues: 418 sheet: 0.13 (0.38), residues: 188 loop : -0.70 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 547 TYR 0.019 0.001 TYR B 487 PHE 0.009 0.001 PHE C 58 TRP 0.038 0.002 TRP A 505 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8513) covalent geometry : angle 0.56224 (11518) hydrogen bonds : bond 0.19020 ( 451) hydrogen bonds : angle 6.38154 ( 1245) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8585 (ttp) cc_final: 0.8323 (ttp) REVERT: B 595 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6591 (ttp-170) REVERT: A 159 MET cc_start: 0.7503 (mmt) cc_final: 0.7229 (tpt) REVERT: A 266 ASP cc_start: 0.8861 (t0) cc_final: 0.8568 (t0) REVERT: A 594 SER cc_start: 0.8005 (m) cc_final: 0.7728 (p) REVERT: C 30 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8411 (pttm) outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.0846 time to fit residues: 16.0569 Evaluate side-chains 124 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 318 GLN A 336 GLN A 403 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106450 restraints weight = 13642.945| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.79 r_work: 0.3421 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8515 Z= 0.115 Angle : 0.535 7.590 11518 Z= 0.276 Chirality : 0.040 0.148 1290 Planarity : 0.004 0.058 1477 Dihedral : 5.382 70.271 1232 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.66 % Allowed : 27.16 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.41 (0.27), residues: 1039 helix: 2.87 (0.25), residues: 426 sheet: 0.03 (0.38), residues: 192 loop : -0.67 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 547 TYR 0.017 0.001 TYR B 487 PHE 0.007 0.001 PHE A 128 TRP 0.019 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8513) covalent geometry : angle 0.53480 (11518) hydrogen bonds : bond 0.04317 ( 451) hydrogen bonds : angle 4.62272 ( 1245) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 280 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: B 365 MET cc_start: 0.8617 (ttp) cc_final: 0.8248 (ttp) REVERT: B 595 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.6505 (ttp-170) REVERT: A 266 ASP cc_start: 0.9307 (t0) cc_final: 0.8951 (t0) REVERT: A 368 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 416 TYR cc_start: 0.7776 (m-80) cc_final: 0.7557 (m-80) REVERT: A 594 SER cc_start: 0.8529 (m) cc_final: 0.8020 (p) REVERT: A 604 MET cc_start: 0.9063 (mmt) cc_final: 0.8861 (mmt) REVERT: A 605 ASP cc_start: 0.9223 (m-30) cc_final: 0.9004 (m-30) REVERT: C 30 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8049 (ttpt) REVERT: C 32 GLN cc_start: 0.8291 (tt0) cc_final: 0.8054 (tp40) outliers start: 24 outliers final: 9 residues processed: 149 average time/residue: 0.0920 time to fit residues: 19.1829 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104443 restraints weight = 13625.460| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.87 r_work: 0.3393 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8515 Z= 0.126 Angle : 0.535 7.847 11518 Z= 0.270 Chirality : 0.039 0.136 1290 Planarity : 0.004 0.056 1477 Dihedral : 5.002 69.917 1226 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.88 % Allowed : 26.05 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.37 (0.27), residues: 1039 helix: 2.84 (0.25), residues: 426 sheet: 0.10 (0.38), residues: 190 loop : -0.75 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 547 TYR 0.014 0.001 TYR B 487 PHE 0.006 0.001 PHE B 117 TRP 0.016 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8513) covalent geometry : angle 0.53541 (11518) hydrogen bonds : bond 0.04267 ( 451) hydrogen bonds : angle 4.32815 ( 1245) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8571 (ttp) cc_final: 0.8271 (ttp) REVERT: B 595 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.6437 (ttp-170) REVERT: A 368 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 594 SER cc_start: 0.8464 (m) cc_final: 0.7969 (p) REVERT: A 601 THR cc_start: 0.7948 (p) cc_final: 0.7676 (m) REVERT: A 605 ASP cc_start: 0.9241 (m-30) cc_final: 0.8952 (m-30) REVERT: A 618 PHE cc_start: 0.6845 (m-80) cc_final: 0.6611 (m-80) REVERT: C 30 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8029 (ttpt) REVERT: C 32 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7957 (tp40) outliers start: 26 outliers final: 15 residues processed: 141 average time/residue: 0.0910 time to fit residues: 18.1262 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 32 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.141104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106669 restraints weight = 13687.316| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.81 r_work: 0.3424 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8515 Z= 0.097 Angle : 0.514 8.213 11518 Z= 0.256 Chirality : 0.039 0.176 1290 Planarity : 0.004 0.056 1477 Dihedral : 4.869 70.333 1226 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.77 % Allowed : 26.50 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.53 (0.28), residues: 1039 helix: 2.99 (0.25), residues: 426 sheet: 0.12 (0.38), residues: 196 loop : -0.66 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 547 TYR 0.012 0.001 TYR A 303 PHE 0.009 0.001 PHE A 551 TRP 0.011 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8513) covalent geometry : angle 0.51406 (11518) hydrogen bonds : bond 0.03721 ( 451) hydrogen bonds : angle 4.14502 ( 1245) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8647 (ttp) cc_final: 0.8354 (ttp) REVERT: B 498 GLN cc_start: 0.9259 (mt0) cc_final: 0.9049 (mt0) REVERT: B 595 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.6382 (ttp-170) REVERT: A 368 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7997 (mm) REVERT: A 594 SER cc_start: 0.8472 (m) cc_final: 0.7981 (p) REVERT: A 601 THR cc_start: 0.7938 (p) cc_final: 0.7700 (m) REVERT: A 605 ASP cc_start: 0.9234 (m-30) cc_final: 0.8965 (m-30) REVERT: C 30 LYS cc_start: 0.8295 (ttpt) cc_final: 0.8057 (ttpp) outliers start: 25 outliers final: 14 residues processed: 146 average time/residue: 0.0908 time to fit residues: 18.6583 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105933 restraints weight = 13674.951| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.79 r_work: 0.3411 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8515 Z= 0.106 Angle : 0.525 7.897 11518 Z= 0.263 Chirality : 0.039 0.178 1290 Planarity : 0.004 0.055 1477 Dihedral : 4.940 71.933 1226 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.10 % Allowed : 27.49 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.54 (0.28), residues: 1039 helix: 2.97 (0.25), residues: 426 sheet: 0.07 (0.38), residues: 205 loop : -0.61 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 547 TYR 0.020 0.001 TYR B 487 PHE 0.006 0.001 PHE B 588 TRP 0.009 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8513) covalent geometry : angle 0.52496 (11518) hydrogen bonds : bond 0.03770 ( 451) hydrogen bonds : angle 4.14907 ( 1245) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 MET cc_start: 0.8672 (ttp) cc_final: 0.8382 (ttp) REVERT: B 498 GLN cc_start: 0.9329 (mt0) cc_final: 0.8957 (mp10) REVERT: B 595 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6435 (ttp-170) REVERT: A 368 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7938 (mm) REVERT: A 594 SER cc_start: 0.8505 (m) cc_final: 0.8016 (p) REVERT: A 601 THR cc_start: 0.7959 (p) cc_final: 0.7662 (m) REVERT: A 605 ASP cc_start: 0.9265 (m-30) cc_final: 0.9003 (m-30) REVERT: A 618 PHE cc_start: 0.6745 (m-80) cc_final: 0.6537 (m-80) REVERT: C 30 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8007 (ttpp) outliers start: 28 outliers final: 18 residues processed: 145 average time/residue: 0.0871 time to fit residues: 17.9404 Evaluate side-chains 140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.138361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103869 restraints weight = 13726.913| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.78 r_work: 0.3401 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8515 Z= 0.135 Angle : 0.550 8.087 11518 Z= 0.274 Chirality : 0.040 0.158 1290 Planarity : 0.004 0.058 1477 Dihedral : 5.206 73.540 1226 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.55 % Allowed : 27.16 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.40 (0.27), residues: 1039 helix: 2.89 (0.25), residues: 426 sheet: 0.03 (0.38), residues: 196 loop : -0.73 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 547 TYR 0.023 0.001 TYR B 487 PHE 0.008 0.001 PHE A 551 TRP 0.009 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8513) covalent geometry : angle 0.55028 (11518) hydrogen bonds : bond 0.04176 ( 451) hydrogen bonds : angle 4.19484 ( 1245) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7910 (mtt) cc_final: 0.7605 (ttm) REVERT: B 365 MET cc_start: 0.8613 (ttp) cc_final: 0.8359 (ttp) REVERT: B 498 GLN cc_start: 0.9288 (mt0) cc_final: 0.8992 (mt0) REVERT: B 595 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.6416 (ttp-170) REVERT: A 303 TYR cc_start: 0.8991 (p90) cc_final: 0.8567 (p90) REVERT: A 368 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 594 SER cc_start: 0.8524 (m) cc_final: 0.8034 (p) REVERT: A 601 THR cc_start: 0.8035 (p) cc_final: 0.7782 (m) REVERT: A 605 ASP cc_start: 0.9280 (m-30) cc_final: 0.8951 (m-30) REVERT: A 618 PHE cc_start: 0.6804 (m-80) cc_final: 0.6467 (m-80) REVERT: C 30 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7946 (ttpp) outliers start: 32 outliers final: 18 residues processed: 151 average time/residue: 0.0809 time to fit residues: 17.3082 Evaluate side-chains 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 0.0010 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101854 restraints weight = 13863.221| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.80 r_work: 0.3353 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8515 Z= 0.156 Angle : 0.569 8.555 11518 Z= 0.284 Chirality : 0.040 0.151 1290 Planarity : 0.004 0.054 1477 Dihedral : 5.403 73.188 1226 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.55 % Allowed : 27.83 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.26 (0.27), residues: 1039 helix: 2.81 (0.25), residues: 426 sheet: -0.12 (0.37), residues: 197 loop : -0.80 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 547 TYR 0.021 0.001 TYR B 487 PHE 0.012 0.002 PHE A 551 TRP 0.039 0.002 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8513) covalent geometry : angle 0.56899 (11518) hydrogen bonds : bond 0.04402 ( 451) hydrogen bonds : angle 4.23463 ( 1245) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7936 (mtt) cc_final: 0.7614 (ttm) REVERT: B 365 MET cc_start: 0.8612 (ttp) cc_final: 0.8329 (ttp) REVERT: B 498 GLN cc_start: 0.9333 (mt0) cc_final: 0.9021 (mt0) REVERT: B 595 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6500 (ttp-170) REVERT: A 594 SER cc_start: 0.8554 (m) cc_final: 0.8070 (p) REVERT: A 601 THR cc_start: 0.8089 (p) cc_final: 0.7813 (m) REVERT: A 605 ASP cc_start: 0.9254 (m-30) cc_final: 0.8908 (m-30) REVERT: A 608 HIS cc_start: 0.8573 (m-70) cc_final: 0.8373 (m-70) REVERT: C 30 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7781 (ttpp) outliers start: 32 outliers final: 22 residues processed: 142 average time/residue: 0.0900 time to fit residues: 17.9378 Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.0000 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 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 = 0.4039 r_free = 0.4039 target = 0.139880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105343 restraints weight = 13730.928| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.81 r_work: 0.3417 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8515 Z= 0.103 Angle : 0.542 8.615 11518 Z= 0.272 Chirality : 0.040 0.297 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.197 73.819 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 29.27 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.41 (0.27), residues: 1039 helix: 2.90 (0.25), residues: 426 sheet: -0.08 (0.37), residues: 205 loop : -0.67 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 547 TYR 0.025 0.001 TYR B 487 PHE 0.014 0.001 PHE A 551 TRP 0.030 0.001 TRP A 505 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8513) covalent geometry : angle 0.54246 (11518) hydrogen bonds : bond 0.03864 ( 451) hydrogen bonds : angle 4.14730 ( 1245) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.7935 (mtt) cc_final: 0.7637 (ttm) REVERT: B 365 MET cc_start: 0.8604 (ttp) cc_final: 0.8392 (ttp) REVERT: B 466 GLN cc_start: 0.8033 (pt0) cc_final: 0.7542 (pm20) REVERT: B 498 GLN cc_start: 0.9283 (mt0) cc_final: 0.8968 (mt0) REVERT: B 595 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6506 (ttp-170) REVERT: A 594 SER cc_start: 0.8450 (m) cc_final: 0.7952 (p) REVERT: A 601 THR cc_start: 0.8014 (p) cc_final: 0.7711 (m) REVERT: A 605 ASP cc_start: 0.9253 (m-30) cc_final: 0.8908 (m-30) REVERT: C 30 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7911 (ttpp) outliers start: 22 outliers final: 15 residues processed: 142 average time/residue: 0.0903 time to fit residues: 18.0893 Evaluate side-chains 137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 584 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099032 restraints weight = 13858.760| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.81 r_work: 0.3302 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8515 Z= 0.228 Angle : 0.648 9.599 11518 Z= 0.324 Chirality : 0.043 0.272 1290 Planarity : 0.005 0.054 1477 Dihedral : 5.659 73.868 1226 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.55 % Allowed : 29.49 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.97 (0.27), residues: 1039 helix: 2.54 (0.25), residues: 426 sheet: -0.30 (0.37), residues: 199 loop : -0.91 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 547 TYR 0.022 0.002 TYR B 487 PHE 0.021 0.002 PHE A 551 TRP 0.028 0.002 TRP A 505 HIS 0.005 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 8513) covalent geometry : angle 0.64800 (11518) hydrogen bonds : bond 0.05165 ( 451) hydrogen bonds : angle 4.47990 ( 1245) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 344 MET cc_start: 0.8399 (tpp) cc_final: 0.8095 (ttm) REVERT: B 365 MET cc_start: 0.8588 (ttp) cc_final: 0.8224 (ttp) REVERT: B 466 GLN cc_start: 0.8117 (pt0) cc_final: 0.7647 (pm20) REVERT: B 498 GLN cc_start: 0.9327 (mt0) cc_final: 0.9033 (mt0) REVERT: B 595 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.6526 (ttp-170) REVERT: A 594 SER cc_start: 0.8551 (m) cc_final: 0.8097 (p) REVERT: A 605 ASP cc_start: 0.9264 (m-30) cc_final: 0.8926 (m-30) REVERT: C 30 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7764 (ttpp) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.0959 time to fit residues: 18.4693 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 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 = 0.4030 r_free = 0.4030 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104754 restraints weight = 13610.566| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.77 r_work: 0.3410 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8515 Z= 0.108 Angle : 0.565 8.976 11518 Z= 0.280 Chirality : 0.041 0.285 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.132 75.149 1226 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.44 % Allowed : 30.04 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.26 (0.27), residues: 1039 helix: 2.81 (0.25), residues: 426 sheet: -0.15 (0.38), residues: 197 loop : -0.79 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 547 TYR 0.023 0.001 TYR B 487 PHE 0.023 0.001 PHE A 618 TRP 0.024 0.001 TRP A 505 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8513) covalent geometry : angle 0.56501 (11518) hydrogen bonds : bond 0.03985 ( 451) hydrogen bonds : angle 4.20795 ( 1245) Misc. bond : bond 0.00037 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 344 MET cc_start: 0.8343 (tpp) cc_final: 0.8001 (ttm) REVERT: B 365 MET cc_start: 0.8609 (ttp) cc_final: 0.8346 (ttp) REVERT: B 466 GLN cc_start: 0.8157 (pt0) cc_final: 0.7632 (pm20) REVERT: B 498 GLN cc_start: 0.9273 (mt0) cc_final: 0.8968 (mt0) REVERT: B 595 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.6603 (ttp-170) REVERT: A 594 SER cc_start: 0.8428 (m) cc_final: 0.7917 (p) REVERT: A 601 THR cc_start: 0.8040 (p) cc_final: 0.7743 (m) REVERT: A 605 ASP cc_start: 0.9243 (m-30) cc_final: 0.8985 (m-30) REVERT: C 30 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7814 (ttpp) outliers start: 13 outliers final: 13 residues processed: 133 average time/residue: 0.0924 time to fit residues: 17.3527 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 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 = 0.4034 r_free = 0.4034 target = 0.139296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104795 restraints weight = 13745.441| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.79 r_work: 0.3414 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8515 Z= 0.108 Angle : 0.556 9.207 11518 Z= 0.275 Chirality : 0.041 0.299 1290 Planarity : 0.004 0.055 1477 Dihedral : 5.057 75.574 1226 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.77 % Allowed : 29.49 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.32 (0.27), residues: 1039 helix: 2.85 (0.25), residues: 426 sheet: -0.07 (0.38), residues: 196 loop : -0.77 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 547 TYR 0.022 0.001 TYR B 487 PHE 0.024 0.001 PHE A 618 TRP 0.025 0.001 TRP A 505 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8513) covalent geometry : angle 0.55602 (11518) hydrogen bonds : bond 0.03844 ( 451) hydrogen bonds : angle 4.12764 ( 1245) Misc. bond : bond 0.00038 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.44 seconds wall clock time: 40 minutes 57.18 seconds (2457.18 seconds total)