Starting phenix.real_space_refine on Sat May 10 01:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtw_37844/05_2025/8wtw_37844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtw_37844/05_2025/8wtw_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_37844/05_2025/8wtw_37844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtw_37844/05_2025/8wtw_37844.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtw_37844/05_2025/8wtw_37844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtw_37844/05_2025/8wtw_37844.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 3 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3.60, per 1000 atoms: 0.79 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: 1.38 Conformation dependent library (CDL) restraints added in 540.0 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: 0.50 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: 1.18 Time building geometry restraints manager: 1.50 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 2.470 nonbonded pdb=" O GLY A 71 " pdb="NA NA A 703 " model vdw 2.305 2.470 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 2.470 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: 1.040 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.050 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 599 PHE 0.018 0.001 PHE A 511 TYR 0.006 0.001 TYR A 575 ARG 0.001 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.31151 ( 247) hydrogen bonds : angle 7.71702 ( 720) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.39487 ( 6) covalent geometry : bond 0.00255 ( 4672) covalent geometry : angle 0.47705 ( 6365) Misc. bond : bond 0.10038 ( 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 : 0.572 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: 0.9359 time to fit residues: 52.5031 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 : 0.466 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 chunk 23 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3476 r_free = 0.3476 target = 0.131676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114440 restraints weight = 5638.751| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.63 r_work: 0.3161 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4677 Z= 0.132 Angle : 0.505 7.663 6371 Z= 0.270 Chirality : 0.039 0.153 707 Planarity : 0.004 0.033 771 Dihedral : 4.009 38.957 613 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.95 % Allowed : 20.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.37), residues: 554 helix: 0.43 (0.27), residues: 379 sheet: 0.43 (2.09), residues: 6 loop : 0.65 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.013 0.001 PHE A 403 TYR 0.008 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.07282 ( 247) hydrogen bonds : angle 4.33933 ( 720) SS BOND : bond 0.00067 ( 3) SS BOND : angle 0.30664 ( 6) covalent geometry : bond 0.00232 ( 4672) covalent geometry : angle 0.50530 ( 6365) Misc. bond : bond 0.00070 ( 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 56 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.452 Fit side-chains REVERT: A 391 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7528 (m-80) outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.8634 time to fit residues: 45.7895 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 : 0.493 ------------------------------------------------------------------------------- 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 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 52 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3512 r_free = 0.3512 target = 0.134309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117470 restraints weight = 5656.155| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.57 r_work: 0.3185 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1893 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= 0.115 Angle : 0.475 7.796 6371 Z= 0.248 Chirality : 0.038 0.150 707 Planarity : 0.004 0.032 771 Dihedral : 3.938 37.924 613 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 20.00 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.37), residues: 554 helix: 0.92 (0.28), residues: 387 sheet: 0.48 (1.87), residues: 6 loop : 0.65 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.000 HIS A 599 PHE 0.013 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05903 ( 247) hydrogen bonds : angle 3.95204 ( 720) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.36363 ( 6) covalent geometry : bond 0.00227 ( 4672) covalent geometry : angle 0.47485 ( 6365) Misc. bond : bond 0.00038 ( 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 51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.406 Fit side-chains REVERT: A 391 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7623 (m-80) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.8509 time to fit residues: 43.4015 Evaluate side-chains 44 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3517 r_free = 0.3517 target = 0.134894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118049 restraints weight = 5623.076| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.56 r_work: 0.3217 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2080 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= 0.102 Angle : 0.446 7.549 6371 Z= 0.232 Chirality : 0.038 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.851 37.755 613 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.89 % Allowed : 20.63 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.38), residues: 554 helix: 1.26 (0.28), residues: 386 sheet: None (None), residues: 0 loop : 0.58 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.009 0.001 TYR A 572 ARG 0.001 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 247) hydrogen bonds : angle 3.74482 ( 720) SS BOND : bond 0.00073 ( 3) SS BOND : angle 0.32649 ( 6) covalent geometry : bond 0.00199 ( 4672) covalent geometry : angle 0.44569 ( 6365) Misc. bond : bond 0.00021 ( 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: 9 poor density : 43 time to evaluate : 0.488 Fit side-chains REVERT: A 391 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7613 (m-80) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.9435 time to fit residues: 49.7455 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114697 restraints weight = 5764.461| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.58 r_work: 0.3172 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4677 Z= 0.127 Angle : 0.487 9.208 6371 Z= 0.253 Chirality : 0.039 0.150 707 Planarity : 0.004 0.030 771 Dihedral : 4.019 38.180 613 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 21.47 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 554 helix: 1.22 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.42 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.002 0.000 HIS A 599 PHE 0.013 0.001 PHE A 362 TYR 0.012 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05807 ( 247) hydrogen bonds : angle 3.75861 ( 720) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.42671 ( 6) covalent geometry : bond 0.00279 ( 4672) covalent geometry : angle 0.48693 ( 6365) Misc. bond : bond 0.00038 ( 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 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.486 Fit side-chains REVERT: A 391 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (m-80) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.8235 time to fit residues: 42.0157 Evaluate side-chains 44 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118352 restraints weight = 5610.838| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.56 r_work: 0.3199 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2179 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= 0.102 Angle : 0.446 8.094 6371 Z= 0.232 Chirality : 0.038 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.923 38.219 613 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 21.05 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.38), residues: 554 helix: 1.38 (0.28), residues: 389 sheet: None (None), residues: 0 loop : 0.51 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.009 0.001 TYR A 572 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 247) hydrogen bonds : angle 3.64867 ( 720) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.31072 ( 6) covalent geometry : bond 0.00205 ( 4672) covalent geometry : angle 0.44630 ( 6365) Misc. bond : bond 0.00017 ( 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 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.452 Fit side-chains REVERT: A 391 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7624 (m-80) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.8268 time to fit residues: 43.0598 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 507 GLN A 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117481 restraints weight = 5655.090| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.57 r_work: 0.3199 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2198 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= 0.102 Angle : 0.448 8.135 6371 Z= 0.232 Chirality : 0.038 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.892 37.688 613 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.11 % Allowed : 21.47 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 554 helix: 1.40 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.50 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 247) hydrogen bonds : angle 3.63829 ( 720) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.33307 ( 6) covalent geometry : bond 0.00207 ( 4672) covalent geometry : angle 0.44766 ( 6365) Misc. bond : bond 0.00016 ( 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 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.514 Fit side-chains REVERT: A 391 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7625 (m-80) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.7848 time to fit residues: 39.3213 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain A residue 282 VAL 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 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3513 r_free = 0.3513 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117747 restraints weight = 5611.274| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.57 r_work: 0.3211 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2236 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= 0.102 Angle : 0.448 8.110 6371 Z= 0.231 Chirality : 0.038 0.151 707 Planarity : 0.003 0.028 771 Dihedral : 3.876 37.588 613 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 21.47 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.38), residues: 554 helix: 1.43 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.55 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 247) hydrogen bonds : angle 3.61955 ( 720) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.32884 ( 6) covalent geometry : bond 0.00208 ( 4672) covalent geometry : angle 0.44770 ( 6365) Misc. bond : bond 0.00016 ( 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 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.497 Fit side-chains REVERT: A 391 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7628 (m-80) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.8212 time to fit residues: 40.2679 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 : 0.498 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain A residue 282 VAL 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 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3495 r_free = 0.3495 target = 0.133044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116229 restraints weight = 5600.836| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.56 r_work: 0.3197 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2184 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= 0.113 Angle : 0.466 8.731 6371 Z= 0.241 Chirality : 0.039 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 3.954 37.909 613 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 21.26 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.38), residues: 554 helix: 1.38 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.53 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 59 HIS 0.002 0.000 HIS A 599 PHE 0.012 0.001 PHE A 362 TYR 0.011 0.001 TYR A 572 ARG 0.001 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 247) hydrogen bonds : angle 3.65925 ( 720) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.36059 ( 6) covalent geometry : bond 0.00243 ( 4672) covalent geometry : angle 0.46648 ( 6365) Misc. bond : bond 0.00020 ( 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 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.455 Fit side-chains REVERT: A 391 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7579 (m-80) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.7938 time to fit residues: 38.9512 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL 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 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3473 r_free = 0.3473 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114240 restraints weight = 5671.732| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.57 r_work: 0.3154 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4677 Z= 0.144 Angle : 0.510 9.981 6371 Z= 0.265 Chirality : 0.040 0.149 707 Planarity : 0.004 0.031 771 Dihedral : 4.191 39.019 613 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.47 % Allowed : 22.11 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.38), residues: 554 helix: 1.28 (0.28), residues: 390 sheet: None (None), residues: 0 loop : 0.38 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.002 0.001 HIS A 599 PHE 0.013 0.002 PHE A 362 TYR 0.012 0.001 TYR A 572 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.06112 ( 247) hydrogen bonds : angle 3.78520 ( 720) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.45222 ( 6) covalent geometry : bond 0.00332 ( 4672) covalent geometry : angle 0.51029 ( 6365) Misc. bond : bond 0.00023 ( 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 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.472 Fit side-chains REVERT: A 391 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7458 (m-80) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.9070 time to fit residues: 40.4787 Evaluate side-chains 42 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 282 VAL 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 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3495 r_free = 0.3495 target = 0.133062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116286 restraints weight = 5624.482| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.56 r_work: 0.3192 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2156 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= 0.110 Angle : 0.467 8.740 6371 Z= 0.242 Chirality : 0.039 0.151 707 Planarity : 0.003 0.029 771 Dihedral : 4.061 38.951 613 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.68 % Allowed : 22.11 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.38), residues: 554 helix: 1.40 (0.28), residues: 391 sheet: None (None), residues: 0 loop : 0.56 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.000 HIS A 599 PHE 0.012 0.001 PHE A 362 TYR 0.010 0.001 TYR A 572 ARG 0.001 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.05225 ( 247) hydrogen bonds : angle 3.69942 ( 720) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.32670 ( 6) covalent geometry : bond 0.00228 ( 4672) covalent geometry : angle 0.46755 ( 6365) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2801.08 seconds wall clock time: 49 minutes 0.03 seconds (2940.03 seconds total)