Starting phenix.real_space_refine on Thu Jul 2 23:29:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk0_38412/07_2026/8xk0_38412.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5720 atoms to isotropic. 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 Mn 2 7.51 5 P 32 5.49 5 S 29 5.16 5 C 3910 2.51 5 N 1116 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 6302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5621 Classifications: {'peptide': 692} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 668} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 298 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 17 Ad-hoc single atom residues: {' MN': 2} Classifications: {'water': 17} Link IDs: {None: 16} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.52, per 1000 atoms: 0.24 Number of scatterers: 6302 At special positions: 0 Unit cell: (74.888, 91.057, 111.481, 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) Mn 2 24.99 S 29 16.00 P 32 15.00 O 1213 8.00 N 1116 7.00 C 3910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 292.0 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 36.6% alpha, 19.9% beta 7 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.748A pdb=" N GLU A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 271 through 290 removed outlier: 3.777A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.508A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.807A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Proline residue: A 410 - end of helix No H-bonds generated for 'chain 'A' and resid 406 through 412' Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.916A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 removed outlier: 3.516A pdb=" N GLU A 477 " --> pdb=" O PRO A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 478 through 488 removed outlier: 3.841A pdb=" N ARG A 482 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 565 through 583 removed outlier: 3.544A pdb=" N GLN A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.920A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.839A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.251A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 234 removed outlier: 3.653A pdb=" N ILE A 231 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 242 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.700A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382 removed outlier: 8.748A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 452 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 419 " --> pdb=" O ILE A 452 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1568 1.33 - 1.45: 1391 1.45 - 1.57: 3414 1.57 - 1.69: 63 1.69 - 1.81: 51 Bond restraints: 6487 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.592 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C3' DG B 11 " pdb=" C2' DG B 11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.96e+00 bond pdb=" C3' DT B 14 " pdb=" C2' DT B 14 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.43e+00 bond pdb=" O3' DT B 1 " pdb=" P DG B 2 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.50e-02 4.44e+03 4.71e+00 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.21e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 8589 1.54 - 3.08: 279 3.08 - 4.61: 30 4.61 - 6.15: 8 6.15 - 7.69: 5 Bond angle restraints: 8911 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.94 -7.69 1.05e+00 9.07e-01 5.37e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 8906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 3625 32.50 - 65.00: 155 65.00 - 97.50: 11 97.50 - 130.00: 0 130.00 - 162.50: 1 Dihedral angle restraints: 3792 sinusoidal: 1750 harmonic: 2042 Sorted by residual: dihedral pdb=" C4' DT B 16 " pdb=" C3' DT B 16 " pdb=" O3' DT B 16 " pdb=" P DA B 17 " ideal model delta sinusoidal sigma weight residual 220.00 57.50 162.50 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta harmonic sigma weight residual 115.10 123.91 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA ASN A 541 " pdb=" C ASN A 541 " pdb=" N VAL A 542 " pdb=" CA VAL A 542 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 3789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 979 0.118 - 0.236: 12 0.236 - 0.355: 1 0.355 - 0.473: 0 0.473 - 0.591: 2 Chirality restraints: 994 Sorted by residual: chirality pdb=" P DA B 17 " pdb=" OP1 DA B 17 " pdb=" OP2 DA B 17 " pdb=" O5' DA B 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" P DT B 16 " pdb=" OP1 DT B 16 " pdb=" OP2 DT B 16 " pdb=" O5' DT B 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 991 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 553 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A 554 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 583 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C GLN A 583 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 583 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 584 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.017 2.00e-02 2.50e+03 8.52e-03 1.82e+00 pdb=" N1 DT B 1 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.003 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 43 2.60 - 3.17: 4972 3.17 - 3.75: 9288 3.75 - 4.32: 13839 4.32 - 4.90: 22613 Nonbonded interactions: 50755 Sorted by model distance: nonbonded pdb=" OP1 DT C 7 " pdb="MN MN A 802 " model vdw 2.023 3.060 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 2.128 3.060 nonbonded pdb=" O GLN A 669 " pdb=" O HOH A 901 " model vdw 2.208 3.040 nonbonded pdb=" OP3 DT B 1 " pdb="MN MN A 801 " model vdw 2.238 3.060 nonbonded pdb=" OD1 ASP A 48 " pdb=" NH2 ARG A 105 " model vdw 2.273 3.120 ... (remaining 50750 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: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.850 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:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.004 0.112 6487 Z= 0.261 Angle : 0.633 7.691 8911 Z= 0.426 Chirality : 0.051 0.591 994 Planarity : 0.004 0.065 1020 Dihedral : 16.436 162.500 2472 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.27 % Favored : 93.44 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: -0.69 (0.32), residues: 686 helix: 0.65 (0.35), residues: 234 sheet: -0.11 (0.41), residues: 162 loop : -1.56 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.020 0.001 TYR A 719 PHE 0.019 0.001 PHE A 682 TRP 0.007 0.001 TRP A 445 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.26 ( 6487) covalent geometry : angle 0.63300 / 0.43 ( 8911) hydrogen bonds : bond 0.18410 / 12.43 ( 246) hydrogen bonds : angle 5.86853 / 4.17 ( 679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.190 Fit side-chains REVERT: A 108 HIS cc_start: 0.6966 (m-70) cc_final: 0.6764 (m90) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.5211 time to fit residues: 56.9094 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 259 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122826 restraints weight = 7278.749| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.86 r_work: 0.3198 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6487 Z= 0.181 Angle : 0.640 8.118 8911 Z= 0.356 Chirality : 0.046 0.243 994 Planarity : 0.004 0.044 1020 Dihedral : 15.785 151.857 1111 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.12 % Favored : 93.44 % Rotamer: Outliers : 1.15 % Allowed : 10.02 % Favored : 88.83 % 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: -0.71 (0.32), residues: 686 helix: 0.60 (0.34), residues: 237 sheet: -0.11 (0.41), residues: 162 loop : -1.58 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 291 TYR 0.011 0.001 TYR A 494 PHE 0.024 0.002 PHE A 401 TRP 0.005 0.001 TRP A 445 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 6487) covalent geometry : angle 0.63964 / 0.36 ( 8911) hydrogen bonds : bond 0.05334 / 3.44 ( 246) hydrogen bonds : angle 4.69111 / 3.38 ( 679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.212 Fit side-chains REVERT: A 67 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6248 (mmt) REVERT: A 108 HIS cc_start: 0.7564 (m-70) cc_final: 0.7337 (m90) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.4491 time to fit residues: 44.2954 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123986 restraints weight = 7282.321| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.93 r_work: 0.3183 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6487 Z= 0.137 Angle : 0.575 7.906 8911 Z= 0.325 Chirality : 0.044 0.210 994 Planarity : 0.004 0.036 1020 Dihedral : 15.639 149.217 1109 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 1.64 % Allowed : 11.82 % Favored : 86.54 % 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: -0.58 (0.32), residues: 686 helix: 0.75 (0.35), residues: 237 sheet: 0.21 (0.43), residues: 146 loop : -1.63 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.011 0.001 TYR A 719 PHE 0.022 0.002 PHE A 319 TRP 0.003 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 6487) covalent geometry : angle 0.57503 / 0.33 ( 8911) hydrogen bonds : bond 0.04309 / 2.78 ( 246) hydrogen bonds : angle 4.48277 / 3.24 ( 679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7532 (m-70) cc_final: 0.7302 (m90) REVERT: A 435 GLN cc_start: 0.8104 (tt0) cc_final: 0.7806 (tp-100) REVERT: A 436 LEU cc_start: 0.8825 (mt) cc_final: 0.8619 (mt) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.4266 time to fit residues: 42.7015 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 467 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122054 restraints weight = 7326.463| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.93 r_work: 0.3173 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6487 Z= 0.163 Angle : 0.588 7.520 8911 Z= 0.331 Chirality : 0.044 0.222 994 Planarity : 0.004 0.038 1020 Dihedral : 15.627 147.061 1109 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 2.13 % Allowed : 12.97 % Favored : 84.89 % 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: -0.61 (0.32), residues: 686 helix: 0.76 (0.35), residues: 237 sheet: 0.33 (0.44), residues: 140 loop : -1.73 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.012 0.001 TYR A 719 PHE 0.023 0.002 PHE A 319 TRP 0.004 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6487) covalent geometry : angle 0.58837 / 0.33 ( 8911) hydrogen bonds : bond 0.04363 / 2.81 ( 246) hydrogen bonds : angle 4.46061 / 3.22 ( 679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7617 (m-70) cc_final: 0.7393 (m90) REVERT: A 435 GLN cc_start: 0.8164 (tt0) cc_final: 0.7832 (tp-100) REVERT: A 436 LEU cc_start: 0.8841 (mt) cc_final: 0.8631 (mt) REVERT: A 720 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7765 (tm-30) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.4473 time to fit residues: 46.0526 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 720 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118750 restraints weight = 7390.862| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.95 r_work: 0.3092 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6487 Z= 0.236 Angle : 0.656 8.000 8911 Z= 0.365 Chirality : 0.047 0.238 994 Planarity : 0.004 0.040 1020 Dihedral : 15.794 146.257 1109 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.12 % Favored : 93.44 % Rotamer: Outliers : 1.64 % Allowed : 14.94 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.32), residues: 686 helix: 0.60 (0.35), residues: 237 sheet: -0.01 (0.41), residues: 155 loop : -1.85 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.013 0.002 TYR A 719 PHE 0.025 0.002 PHE A 319 TRP 0.006 0.001 TRP A 512 HIS 0.015 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 6487) covalent geometry : angle 0.65561 / 0.36 ( 8911) hydrogen bonds : bond 0.05130 / 3.27 ( 246) hydrogen bonds : angle 4.66226 / 3.36 ( 679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7666 (m-70) cc_final: 0.7435 (m90) REVERT: A 435 GLN cc_start: 0.8226 (tt0) cc_final: 0.7873 (tp-100) REVERT: A 578 LYS cc_start: 0.8274 (mmmm) cc_final: 0.8000 (mmmm) REVERT: A 720 GLN cc_start: 0.8005 (tp40) cc_final: 0.7789 (tp-100) outliers start: 10 outliers final: 3 residues processed: 89 average time/residue: 0.4452 time to fit residues: 42.1164 Evaluate side-chains 83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122129 restraints weight = 7321.286| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.91 r_work: 0.3185 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6487 Z= 0.137 Angle : 0.572 7.142 8911 Z= 0.324 Chirality : 0.044 0.202 994 Planarity : 0.004 0.039 1020 Dihedral : 15.673 145.544 1109 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.25 % Favored : 94.31 % Rotamer: Outliers : 2.46 % Allowed : 15.44 % Favored : 82.10 % 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: -0.57 (0.32), residues: 686 helix: 0.80 (0.35), residues: 237 sheet: 0.26 (0.43), residues: 146 loop : -1.69 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.014 0.001 TYR A 719 PHE 0.020 0.002 PHE A 319 TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 6487) covalent geometry : angle 0.57186 / 0.32 ( 8911) hydrogen bonds : bond 0.03950 / 2.54 ( 246) hydrogen bonds : angle 4.45901 / 3.22 ( 679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.201 Fit side-chains REVERT: A 108 HIS cc_start: 0.7536 (m-70) cc_final: 0.7326 (m90) REVERT: A 435 GLN cc_start: 0.8161 (tt0) cc_final: 0.7817 (tp-100) REVERT: A 436 LEU cc_start: 0.8841 (mt) cc_final: 0.8636 (mt) REVERT: A 578 LYS cc_start: 0.8225 (mmmm) cc_final: 0.7950 (mmmm) outliers start: 15 outliers final: 6 residues processed: 96 average time/residue: 0.3960 time to fit residues: 40.5961 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122462 restraints weight = 7274.219| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.81 r_work: 0.3192 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6487 Z= 0.160 Angle : 0.596 8.187 8911 Z= 0.334 Chirality : 0.044 0.214 994 Planarity : 0.004 0.039 1020 Dihedral : 15.655 144.475 1109 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.88 % Rotamer: Outliers : 2.13 % Allowed : 16.91 % Favored : 80.95 % 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: -0.63 (0.32), residues: 686 helix: 0.80 (0.35), residues: 237 sheet: 0.37 (0.44), residues: 140 loop : -1.82 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.014 0.001 TYR A 719 PHE 0.022 0.002 PHE A 319 TRP 0.004 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 6487) covalent geometry : angle 0.59609 / 0.33 ( 8911) hydrogen bonds : bond 0.04172 / 2.66 ( 246) hydrogen bonds : angle 4.44227 / 3.21 ( 679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7539 (m-70) cc_final: 0.7314 (m90) REVERT: A 427 SER cc_start: 0.7381 (OUTLIER) cc_final: 0.7076 (t) REVERT: A 435 GLN cc_start: 0.8170 (tt0) cc_final: 0.7810 (tp-100) REVERT: A 436 LEU cc_start: 0.8829 (mt) cc_final: 0.8610 (mt) REVERT: A 578 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7930 (mmmm) REVERT: A 721 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7760 (mtt180) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.4407 time to fit residues: 44.8873 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 701 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118204 restraints weight = 7306.453| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.94 r_work: 0.3090 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6487 Z= 0.250 Angle : 0.682 8.585 8911 Z= 0.377 Chirality : 0.048 0.239 994 Planarity : 0.004 0.040 1020 Dihedral : 15.880 143.961 1109 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.88 % Rotamer: Outliers : 2.13 % Allowed : 17.57 % Favored : 80.30 % 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: -0.88 (0.32), residues: 686 helix: 0.54 (0.35), residues: 237 sheet: -0.03 (0.41), residues: 161 loop : -1.88 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.014 0.002 TYR A 719 PHE 0.026 0.002 PHE A 319 TRP 0.008 0.002 TRP A 512 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 ( 6487) covalent geometry : angle 0.68201 / 0.38 ( 8911) hydrogen bonds : bond 0.05312 / 3.37 ( 246) hydrogen bonds : angle 4.70227 / 3.39 ( 679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7301 (ttt) REVERT: A 108 HIS cc_start: 0.7732 (m-70) cc_final: 0.7530 (m90) REVERT: A 427 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7224 (p) REVERT: A 435 GLN cc_start: 0.8294 (tt0) cc_final: 0.7873 (tp-100) REVERT: A 721 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7858 (mtt180) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.4254 time to fit residues: 42.1003 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 701 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 20 optimal weight: 0.0030 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124250 restraints weight = 7339.353| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.92 r_work: 0.3219 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6487 Z= 0.126 Angle : 0.579 8.598 8911 Z= 0.326 Chirality : 0.043 0.182 994 Planarity : 0.004 0.039 1020 Dihedral : 15.621 143.074 1109 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.81 % Favored : 94.75 % Rotamer: Outliers : 1.64 % Allowed : 17.73 % Favored : 80.62 % 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: -0.52 (0.32), residues: 686 helix: 0.93 (0.35), residues: 234 sheet: 0.24 (0.43), residues: 146 loop : -1.69 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.016 0.001 TYR A 719 PHE 0.019 0.001 PHE A 319 TRP 0.008 0.001 TRP A 445 HIS 0.009 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 6487) covalent geometry : angle 0.57858 / 0.33 ( 8911) hydrogen bonds : bond 0.03529 / 2.25 ( 246) hydrogen bonds : angle 4.41224 / 3.19 ( 679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7509 (m-70) cc_final: 0.7306 (m90) REVERT: A 371 LYS cc_start: 0.8865 (tptt) cc_final: 0.8599 (tptp) REVERT: A 427 SER cc_start: 0.7428 (OUTLIER) cc_final: 0.7071 (t) REVERT: A 435 GLN cc_start: 0.8204 (tt0) cc_final: 0.7821 (tp-100) REVERT: A 721 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7752 (mtt180) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.4417 time to fit residues: 43.5976 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127739 restraints weight = 7088.352| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.72 r_work: 0.3294 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.138 Angle : 0.590 9.562 8911 Z= 0.328 Chirality : 0.044 0.201 994 Planarity : 0.004 0.039 1020 Dihedral : 15.528 141.941 1109 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.96 % Favored : 94.61 % Rotamer: Outliers : 1.15 % Allowed : 19.05 % Favored : 79.80 % 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: -0.51 (0.32), residues: 686 helix: 0.87 (0.35), residues: 234 sheet: 0.49 (0.44), residues: 145 loop : -1.75 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.014 0.001 TYR A 719 PHE 0.020 0.001 PHE A 319 TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 6487) covalent geometry : angle 0.59044 / 0.33 ( 8911) hydrogen bonds : bond 0.03731 / 2.39 ( 246) hydrogen bonds : angle 4.43803 / 3.19 ( 679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 427 SER cc_start: 0.7376 (t) cc_final: 0.6954 (p) REVERT: A 435 GLN cc_start: 0.8141 (tt0) cc_final: 0.7771 (tp-100) REVERT: A 721 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7775 (mtt180) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.4506 time to fit residues: 43.5626 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129490 restraints weight = 7152.102| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.93 r_work: 0.3302 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6487 Z= 0.127 Angle : 0.586 11.413 8911 Z= 0.323 Chirality : 0.043 0.191 994 Planarity : 0.004 0.041 1020 Dihedral : 15.458 141.020 1109 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.81 % Favored : 94.75 % Rotamer: Outliers : 1.15 % Allowed : 19.21 % Favored : 79.64 % 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: -0.57 (0.32), residues: 686 helix: 0.83 (0.35), residues: 234 sheet: 0.61 (0.45), residues: 134 loop : -1.82 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.013 0.001 TYR A 719 PHE 0.019 0.001 PHE A 319 TRP 0.004 0.001 TRP A 445 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 6487) covalent geometry : angle 0.58558 / 0.32 ( 8911) hydrogen bonds : bond 0.03531 / 2.27 ( 246) hydrogen bonds : angle 4.41119 / 3.17 ( 679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.13 seconds wall clock time: 40 minutes 15.47 seconds (2415.47 seconds total)