Starting phenix.real_space_refine on Thu Jul 2 00:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtw_37844/07_2026/8wtw_37844.cif" } resolution = 2.8 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= -0.001 sd= 0.053 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: 6 Type Number sf(0) Gaussians S 24 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3034 2.51 5 N 708 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4415 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 531} Chain breaks: 1 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 99 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Chain breaks: 3 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0A1:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.50, per 1000 atoms: 0.33 Number of scatterers: 4531 At special positions: 0 Unit cell: (73.1, 68.85, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 24 16.00 Na 2 11.00 O 762 8.00 N 708 7.00 C 3034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 11 " distance=2.03 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: 0.53 Conformation dependent library (CDL) restraints added in 192.6 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 77.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.918A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.650A pdb=" N ARG A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.563A pdb=" N GLY A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.544A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.149A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 4.024A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.739A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.619A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.598A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.687A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.524A pdb=" N ARG A 301 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 303' Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.090A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.861A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 344 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.578A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 402 through 433 removed outlier: 3.511A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.641A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.784A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.528A pdb=" N MET A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.520A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.957A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.780A pdb=" N VAL A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.759A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.883A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 600 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.159A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 247 hydrogen bonds defined for protein. 720 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: 0.77 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: 1.18 - 1.31: 666 1.31 - 1.43: 1459 1.43 - 1.56: 2510 1.56 - 1.68: 2 1.68 - 1.81: 35 Bond restraints: 4672 Sorted by residual: bond pdb=" C ARG B 12 " pdb=" N HYP B 13 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.13e+00 bond pdb=" CZ 0A1 B 101 " pdb=" OH 0A1 B 101 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CA HYP B 13 " pdb=" C HYP B 13 " ideal model delta sigma weight residual 1.525 1.577 -0.052 2.10e-02 2.27e+03 6.04e+00 bond pdb=" C 0A1 B 101 " pdb=" O 0A1 B 101 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" CA ARG B 12 " pdb=" C ARG B 12 " ideal model delta sigma weight residual 1.525 1.573 -0.048 2.10e-02 2.27e+03 5.13e+00 ... (remaining 4667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6312 2.00 - 4.00: 39 4.00 - 5.99: 12 5.99 - 7.99: 0 7.99 - 9.99: 2 Bond angle restraints: 6365 Sorted by residual: angle pdb=" N HYP B 13 " pdb=" CA HYP B 13 " pdb=" CB HYP B 13 " ideal model delta sigma weight residual 103.00 108.02 -5.02 1.10e+00 8.26e-01 2.08e+01 angle pdb=" N HYP B 13 " pdb=" CD HYP B 13 " pdb=" CG HYP B 13 " ideal model delta sigma weight residual 103.20 108.53 -5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA 0A1 B 101 " pdb=" CB 0A1 B 101 " pdb=" CG 0A1 B 101 " ideal model delta sigma weight residual 118.13 109.10 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA CYS B 11 " pdb=" C CYS B 11 " pdb=" N ARG B 12 " ideal model delta sigma weight residual 116.01 113.08 2.93 1.49e+00 4.50e-01 3.88e+00 angle pdb=" CA ASP A 298 " pdb=" C ASP A 298 " pdb=" O ASP A 298 " ideal model delta sigma weight residual 120.47 118.04 2.43 1.35e+00 5.49e-01 3.25e+00 ... (remaining 6360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 2282 18.00 - 36.00: 256 36.00 - 54.00: 66 54.00 - 72.00: 8 72.00 - 90.00: 6 Dihedral angle restraints: 2618 sinusoidal: 989 harmonic: 1629 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -51.94 -34.06 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" CB GLU A 122 " pdb=" CG GLU A 122 " pdb=" CD GLU A 122 " pdb=" OE1 GLU A 122 " ideal model delta sinusoidal sigma weight residual 0.00 90.00 -90.00 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CG ARG A 440 " pdb=" CD ARG A 440 " pdb=" NE ARG A 440 " pdb=" CZ ARG A 440 " ideal model delta sinusoidal sigma weight residual -90.00 -133.70 43.70 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 2615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 375 0.023 - 0.046: 184 0.046 - 0.069: 110 0.069 - 0.092: 17 0.092 - 0.115: 21 Chirality restraints: 707 Sorted by residual: chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CG HYP B 13 " pdb=" CB HYP B 13 " pdb=" CD HYP B 13 " pdb=" OD1 HYP B 13 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.11 2.00e-01 2.50e+01 3.25e-01 chirality pdb=" CA PHE A 82 " pdb=" N PHE A 82 " pdb=" C PHE A 82 " pdb=" CB PHE A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 704 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 11 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C CYS B 11 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS B 11 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 12 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 107 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 108 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 512 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 513 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " -0.019 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1366 2.81 - 3.33: 3953 3.33 - 3.86: 6934 3.86 - 4.38: 8668 4.38 - 4.90: 14827 Nonbonded interactions: 35748 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 702 " model vdw 2.289 3.210 nonbonded pdb=" O GLY A 71 " pdb="NA NA A 703 " model vdw 2.305 3.210 nonbonded pdb=" O ARG A 442 " pdb=" OG1 THR A 446 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASN A 78 " pdb="NA NA A 702 " model vdw 2.318 3.210 nonbonded pdb=" O ILE A 349 " pdb=" OG1 THR A 353 " model vdw 2.319 3.040 ... (remaining 35743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.250 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 0.101 4677 Z= 0.244 Angle : 0.477 9.989 6371 Z= 0.239 Chirality : 0.036 0.115 707 Planarity : 0.004 0.039 771 Dihedral : 16.197 90.005 1571 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 21.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.28 (0.34), residues: 554 helix: -1.31 (0.24), residues: 361 sheet: 1.28 (2.52), residues: 6 loop : 0.55 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 607 TYR 0.006 0.001 TYR A 575 PHE 0.018 0.001 PHE A 511 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 4672) covalent geometry : angle 0.47705 / 0.24 ( 6365) SS BOND : bond 0.00075 / 0.04 ( 3) SS BOND : angle 0.39487 / 0.26 ( 6) hydrogen bonds : bond 0.31151 / 20.61 ( 247) hydrogen bonds : angle 7.71702 / 5.70 ( 720) Misc. bond : bond 0.10038 / 6.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.172 Fit side-chains REVERT: A 377 GLU cc_start: 0.7801 (mp0) cc_final: 0.7172 (mp0) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.4524 time to fit residues: 25.2211 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.0030 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113902 restraints weight = 5728.362| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.64 r_work: 0.3175 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4677 Z= 0.134 Angle : 0.524 8.041 6371 Z= 0.281 Chirality : 0.040 0.150 707 Planarity : 0.004 0.034 771 Dihedral : 4.044 39.033 613 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.16 % Allowed : 19.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.37), residues: 554 helix: 0.47 (0.27), residues: 379 sheet: 0.36 (2.05), residues: 6 loop : 0.65 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.009 0.001 TYR A 572 PHE 0.014 0.001 PHE A 403 TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 4672) covalent geometry : angle 0.52366 / 0.28 ( 6365) SS BOND : bond 0.00068 / 0.04 ( 3) SS BOND : angle 0.34602 / 0.24 ( 6) hydrogen bonds : bond 0.07156 / 4.72 ( 247) hydrogen bonds : angle 4.34096 / 3.20 ( 720) Misc. bond : bond 0.00077 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.173 Fit side-chains REVERT: A 391 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7519 (m-80) outliers start: 15 outliers final: 8 residues processed: 52 average time/residue: 0.3961 time to fit residues: 21.8119 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111356 restraints weight = 5658.340| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.58 r_work: 0.3117 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4677 Z= 0.166 Angle : 0.556 10.404 6371 Z= 0.291 Chirality : 0.041 0.149 707 Planarity : 0.004 0.037 771 Dihedral : 4.273 39.036 613 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.58 % Allowed : 19.58 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.94 (0.37), residues: 554 helix: 0.85 (0.28), residues: 379 sheet: 0.06 (1.83), residues: 6 loop : 0.43 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.013 0.001 TYR A 572 PHE 0.017 0.002 PHE A 362 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4672) covalent geometry : angle 0.55550 / 0.29 ( 6365) SS BOND : bond 0.00189 / 0.13 ( 3) SS BOND : angle 0.57369 / 0.41 ( 6) hydrogen bonds : bond 0.07383 / 4.80 ( 247) hydrogen bonds : angle 4.12921 / 3.03 ( 720) Misc. bond : bond 0.00080 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.169 Fit side-chains REVERT: A 391 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7446 (m-80) outliers start: 17 outliers final: 13 residues processed: 51 average time/residue: 0.3996 time to fit residues: 21.5537 Evaluate side-chains 51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115945 restraints weight = 5679.459| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.57 r_work: 0.3163 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4677 Z= 0.120 Angle : 0.485 9.279 6371 Z= 0.253 Chirality : 0.039 0.150 707 Planarity : 0.004 0.033 771 Dihedral : 4.136 39.255 613 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.32 % Allowed : 21.68 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.20 (0.38), residues: 554 helix: 1.07 (0.28), residues: 386 sheet: None (None), residues: 0 loop : 0.41 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 56 TYR 0.011 0.001 TYR A 572 PHE 0.012 0.001 PHE A 362 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 4672) covalent geometry : angle 0.48464 / 0.25 ( 6365) SS BOND : bond 0.00086 / 0.06 ( 3) SS BOND : angle 0.39359 / 0.28 ( 6) hydrogen bonds : bond 0.05768 / 3.75 ( 247) hydrogen bonds : angle 3.90368 / 2.86 ( 720) Misc. bond : bond 0.00024 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.178 Fit side-chains REVERT: A 391 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7500 (m-80) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.4182 time to fit residues: 21.7068 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113952 restraints weight = 5695.893| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.57 r_work: 0.3170 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4677 Z= 0.129 Angle : 0.497 9.641 6371 Z= 0.259 Chirality : 0.039 0.150 707 Planarity : 0.004 0.033 771 Dihedral : 4.157 38.809 613 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.16 % Allowed : 21.26 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.38), residues: 554 helix: 1.15 (0.28), residues: 386 sheet: None (None), residues: 0 loop : 0.39 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.012 0.001 TYR A 572 PHE 0.013 0.001 PHE A 362 TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4672) covalent geometry : angle 0.49655 / 0.26 ( 6365) SS BOND : bond 0.00121 / 0.08 ( 3) SS BOND : angle 0.44725 / 0.32 ( 6) hydrogen bonds : bond 0.05954 / 3.87 ( 247) hydrogen bonds : angle 3.84742 / 2.83 ( 720) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.169 Fit side-chains REVERT: A 391 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7519 (m-80) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 0.4379 time to fit residues: 24.0393 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113959 restraints weight = 5812.662| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.59 r_work: 0.3157 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4677 Z= 0.127 Angle : 0.491 9.764 6371 Z= 0.256 Chirality : 0.039 0.150 707 Planarity : 0.004 0.031 771 Dihedral : 4.168 38.752 613 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.74 % Allowed : 21.89 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.38), residues: 554 helix: 1.17 (0.28), residues: 388 sheet: None (None), residues: 0 loop : 0.30 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.011 0.001 TYR A 572 PHE 0.013 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4672) covalent geometry : angle 0.49119 / 0.26 ( 6365) SS BOND : bond 0.00124 / 0.08 ( 3) SS BOND : angle 0.43072 / 0.31 ( 6) hydrogen bonds : bond 0.05798 / 3.77 ( 247) hydrogen bonds : angle 3.80370 / 2.79 ( 720) Misc. bond : bond 0.00023 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.161 Fit side-chains REVERT: A 391 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7472 (m-80) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 0.4152 time to fit residues: 22.4350 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116580 restraints weight = 5670.331| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.57 r_work: 0.3185 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4677 Z= 0.110 Angle : 0.469 8.906 6371 Z= 0.243 Chirality : 0.038 0.151 707 Planarity : 0.004 0.030 771 Dihedral : 4.061 38.316 613 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.16 % Allowed : 21.68 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.38), residues: 554 helix: 1.26 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.39 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.010 0.001 TYR A 572 PHE 0.011 0.001 PHE A 362 TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 4672) covalent geometry : angle 0.46886 / 0.24 ( 6365) SS BOND : bond 0.00094 / 0.06 ( 3) SS BOND : angle 0.38227 / 0.27 ( 6) hydrogen bonds : bond 0.05208 / 3.38 ( 247) hydrogen bonds : angle 3.73175 / 2.74 ( 720) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.177 Fit side-chains REVERT: A 391 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7546 (m-80) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 0.3494 time to fit residues: 19.7689 Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115603 restraints weight = 5740.253| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.57 r_work: 0.3182 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4677 Z= 0.114 Angle : 0.472 9.049 6371 Z= 0.245 Chirality : 0.038 0.151 707 Planarity : 0.004 0.030 771 Dihedral : 4.050 38.207 613 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 21.68 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.38), residues: 554 helix: 1.28 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.43 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.011 0.001 TYR A 572 PHE 0.012 0.001 PHE A 362 TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 4672) covalent geometry : angle 0.47205 / 0.24 ( 6365) SS BOND : bond 0.00100 / 0.07 ( 3) SS BOND : angle 0.39502 / 0.28 ( 6) hydrogen bonds : bond 0.05291 / 3.43 ( 247) hydrogen bonds : angle 3.71896 / 2.73 ( 720) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.123 Fit side-chains REVERT: A 391 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7563 (m-80) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.3114 time to fit residues: 16.6235 Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114206 restraints weight = 5629.320| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.57 r_work: 0.3153 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4677 Z= 0.138 Angle : 0.506 10.067 6371 Z= 0.263 Chirality : 0.040 0.150 707 Planarity : 0.004 0.031 771 Dihedral : 4.192 38.786 613 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.16 % Allowed : 21.05 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.38), residues: 554 helix: 1.22 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.33 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.012 0.001 TYR A 572 PHE 0.013 0.001 PHE A 362 TRP 0.007 0.001 TRP A 59 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4672) covalent geometry : angle 0.50614 / 0.26 ( 6365) SS BOND : bond 0.00143 / 0.10 ( 3) SS BOND : angle 0.46656 / 0.33 ( 6) hydrogen bonds : bond 0.05955 / 3.87 ( 247) hydrogen bonds : angle 3.79338 / 2.79 ( 720) Misc. bond : bond 0.00024 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.179 Fit side-chains REVERT: A 391 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7462 (m-80) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.3829 time to fit residues: 20.7656 Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 350 ASN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117156 restraints weight = 5629.170| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.55 r_work: 0.3203 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4677 Z= 0.104 Angle : 0.457 8.682 6371 Z= 0.237 Chirality : 0.038 0.151 707 Planarity : 0.004 0.029 771 Dihedral : 4.118 38.483 613 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.11 % Allowed : 22.11 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.38), residues: 554 helix: 1.36 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.49 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 56 TYR 0.010 0.001 TYR A 572 PHE 0.011 0.001 PHE A 362 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 4672) covalent geometry : angle 0.45666 / 0.24 ( 6365) SS BOND : bond 0.00077 / 0.05 ( 3) SS BOND : angle 0.34555 / 0.24 ( 6) hydrogen bonds : bond 0.04884 / 3.17 ( 247) hydrogen bonds : angle 3.68819 / 2.70 ( 720) Misc. bond : bond 0.00002 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.172 Fit side-chains REVERT: A 391 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7484 (m-80) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.3325 time to fit residues: 16.6866 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN A 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108022 restraints weight = 5630.761| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.66 r_work: 0.3126 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4677 Z= 0.146 Angle : 0.516 10.314 6371 Z= 0.268 Chirality : 0.040 0.150 707 Planarity : 0.004 0.031 771 Dihedral : 4.270 38.827 613 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.89 % Allowed : 22.53 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.38), residues: 554 helix: 1.25 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.37 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.012 0.001 TYR A 572 PHE 0.013 0.001 PHE A 362 TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4672) covalent geometry : angle 0.51619 / 0.27 ( 6365) SS BOND : bond 0.00155 / 0.10 ( 3) SS BOND : angle 0.49218 / 0.35 ( 6) hydrogen bonds : bond 0.06093 / 3.96 ( 247) hydrogen bonds : angle 3.80195 / 2.79 ( 720) Misc. bond : bond 0.00022 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1369.36 seconds wall clock time: 24 minutes 8.38 seconds (1448.38 seconds total)