Starting phenix.real_space_refine on Wed Aug 5 17:14:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk0_38412/08_2026/8xk0_38412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk0_38412/08_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_38412/08_2026/8xk0_38412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_2026/8xk0_38412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_2026/8xk0_38412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_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-2.2rc3-6140/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, 19 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2, 'water': 17} Link IDs: {None: 18} 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: 1.32, per 1000 atoms: 0.21 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: 0.48 Conformation dependent library (CDL) restraints added in 320.9 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: 0.63 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: 1.02 Time building geometry restraints manager: 0.66 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=" O3' DT B 1 " pdb=" P DG B 2 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.20e-02 6.94e+03 7.36e+00 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=" 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 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 2.128 2.320 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 2.320 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.040 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:5.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- 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= 0.262 Angle : 0.634 7.691 8911 Z= 0.428 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 0.63439 / 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 : 0.221 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: 0.4983 time to fit residues: 54.4864 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 : 0.276 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.159937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122827 restraints weight = 7291.880| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.83 r_work: 0.3187 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1001 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 8.403 8911 Z= 0.357 Chirality : 0.046 0.259 994 Planarity : 0.004 0.044 1020 Dihedral : 15.793 152.361 1111 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.03 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: -0.10 (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 0.026 0.002 PHE A 401 TRP 0.006 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 0.63958 / 0.36 ( 8911) hydrogen bonds : bond 0.05282 / 3.39 ( 246) hydrogen bonds : angle 4.69253 / 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 : 0.224 Fit side-chains REVERT: A 67 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6230 (mmt) REVERT: A 108 HIS cc_start: 0.7555 (m-70) cc_final: 0.7309 (m90) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.4450 time to fit residues: 44.0008 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.158426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120674 restraints weight = 7293.007| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.94 r_work: 0.3112 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1247 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= 0.183 Angle : 0.615 8.524 8911 Z= 0.346 Chirality : 0.046 0.247 994 Planarity : 0.004 0.039 1020 Dihedral : 15.761 148.996 1109 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.83 % Favored : 93.73 % Rotamer: Outliers : 1.64 % Allowed : 12.15 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.74 (0.32), residues: 686 helix: 0.61 (0.35), residues: 239 sheet: 0.17 (0.43), residues: 146 loop : -1.76 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.012 0.001 TYR A 719 PHE 0.025 0.002 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 6487) covalent geometry : angle 0.61520 / 0.35 ( 8911) hydrogen bonds : bond 0.04928 / 3.16 ( 246) hydrogen bonds : angle 4.60582 / 3.32 ( 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 100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7653 (m-70) cc_final: 0.7409 (m90) REVERT: A 435 GLN cc_start: 0.8147 (tt0) cc_final: 0.7842 (tp-100) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.4143 time to fit residues: 42.4248 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 0.0570 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122518 restraints weight = 7331.480| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.93 r_work: 0.3184 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.138 Angle : 0.572 7.337 8911 Z= 0.325 Chirality : 0.044 0.224 994 Planarity : 0.004 0.038 1020 Dihedral : 15.657 147.380 1109 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 1.81 % Allowed : 14.45 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.32), residues: 686 helix: 0.76 (0.35), residues: 237 sheet: 0.36 (0.44), residues: 140 loop : -1.76 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.012 0.001 TYR A 719 PHE 0.021 0.002 PHE A 319 TRP 0.005 0.001 TRP A 445 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 6487) covalent geometry : angle 0.57202 / 0.32 ( 8911) hydrogen bonds : bond 0.04058 / 2.62 ( 246) hydrogen bonds : angle 4.44893 / 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 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7579 (m-70) cc_final: 0.7356 (m90) REVERT: A 435 GLN cc_start: 0.8164 (tt0) cc_final: 0.7839 (tp-100) REVERT: A 436 LEU cc_start: 0.8841 (mt) cc_final: 0.8631 (mt) REVERT: A 720 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7759 (tm-30) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.4150 time to fit residues: 40.5323 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 : 0.164 ------------------------------------------------------------------------------- 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 73 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 572 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.159923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122119 restraints weight = 7388.035| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.94 r_work: 0.3161 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6487 Z= 0.146 Angle : 0.573 7.263 8911 Z= 0.323 Chirality : 0.044 0.228 994 Planarity : 0.003 0.038 1020 Dihedral : 15.610 145.885 1109 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.88 % 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: -0.57 (0.32), residues: 686 helix: 0.82 (0.35), residues: 237 sheet: 0.41 (0.44), residues: 140 loop : -1.77 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.013 0.001 TYR A 719 PHE 0.022 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 0.00302 / 0.15 ( 6487) covalent geometry : angle 0.57279 / 0.32 ( 8911) hydrogen bonds : bond 0.04052 / 2.61 ( 246) hydrogen bonds : angle 4.40890 / 3.19 ( 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 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.151 Fit side-chains REVERT: A 108 HIS cc_start: 0.7620 (m-70) cc_final: 0.7415 (m90) REVERT: A 435 GLN cc_start: 0.8175 (tt0) cc_final: 0.7825 (tp-100) REVERT: A 436 LEU cc_start: 0.8852 (mt) cc_final: 0.8638 (mt) REVERT: A 578 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7954 (mmmm) REVERT: A 721 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7781 (mtt180) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.4148 time to fit residues: 40.1256 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 437 LEU 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.157845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120163 restraints weight = 7325.726| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.92 r_work: 0.3150 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6487 Z= 0.193 Angle : 0.617 8.229 8911 Z= 0.345 Chirality : 0.046 0.239 994 Planarity : 0.004 0.039 1020 Dihedral : 15.706 145.143 1109 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.88 % Rotamer: Outliers : 2.30 % Allowed : 15.60 % 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: -0.73 (0.32), residues: 686 helix: 0.68 (0.35), residues: 239 sheet: 0.33 (0.44), residues: 140 loop : -1.87 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 175 TYR 0.014 0.001 TYR A 719 PHE 0.023 0.002 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 6487) covalent geometry : angle 0.61658 / 0.34 ( 8911) hydrogen bonds : bond 0.04522 / 2.88 ( 246) hydrogen bonds : angle 4.50910 / 3.26 ( 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 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.171 Fit side-chains REVERT: A 108 HIS cc_start: 0.7599 (m-70) cc_final: 0.7384 (m90) REVERT: A 435 GLN cc_start: 0.8213 (tt0) cc_final: 0.7843 (tp-100) REVERT: A 436 LEU cc_start: 0.8861 (mt) cc_final: 0.8638 (mt) REVERT: A 578 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7982 (mmmm) REVERT: A 725 MET cc_start: 0.5165 (mmp) cc_final: 0.4155 (tpp) outliers start: 14 outliers final: 6 residues processed: 94 average time/residue: 0.3741 time to fit residues: 37.4977 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 : 0.154 ------------------------------------------------------------------------------- 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 73 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121127 restraints weight = 7288.280| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.91 r_work: 0.3165 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.159 Angle : 0.595 8.524 8911 Z= 0.335 Chirality : 0.045 0.225 994 Planarity : 0.004 0.040 1020 Dihedral : 15.682 144.475 1109 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 2.30 % Allowed : 16.09 % Favored : 81.61 % 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: 0.81 (0.35), residues: 237 sheet: 0.35 (0.44), residues: 140 loop : -1.80 (0.33), residues: 309 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 0.021 0.002 PHE A 319 TRP 0.003 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 0.59542 / 0.33 ( 8911) hydrogen bonds : bond 0.04170 / 2.67 ( 246) hydrogen bonds : angle 4.44375 / 3.22 ( 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 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7568 (m-70) cc_final: 0.7338 (m90) REVERT: A 427 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7107 (t) REVERT: A 435 GLN cc_start: 0.8220 (tt0) cc_final: 0.7853 (tp-100) REVERT: A 436 LEU cc_start: 0.8849 (mt) cc_final: 0.8633 (mt) REVERT: A 720 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7756 (tm-30) REVERT: A 721 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7783 (mtt180) outliers start: 14 outliers final: 7 residues processed: 98 average time/residue: 0.4024 time to fit residues: 41.9274 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 : 0.238 ------------------------------------------------------------------------------- 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 73 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119611 restraints weight = 7287.292| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.93 r_work: 0.3125 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6487 Z= 0.207 Angle : 0.642 8.543 8911 Z= 0.357 Chirality : 0.047 0.241 994 Planarity : 0.004 0.040 1020 Dihedral : 15.769 143.737 1109 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.83 % Favored : 93.73 % Rotamer: Outliers : 2.30 % Allowed : 17.57 % Favored : 80.13 % 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: -0.75 (0.32), residues: 686 helix: 0.67 (0.35), residues: 239 sheet: 0.29 (0.44), residues: 145 loop : -1.90 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 175 TYR 0.015 0.002 TYR A 719 PHE 0.024 0.002 PHE A 319 TRP 0.006 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 6487) covalent geometry : angle 0.64209 / 0.36 ( 8911) hydrogen bonds : bond 0.04749 / 3.02 ( 246) hydrogen bonds : angle 4.59071 / 3.31 ( 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 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7659 (m-70) cc_final: 0.7457 (m90) REVERT: A 427 SER cc_start: 0.7551 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 435 GLN cc_start: 0.8282 (tt0) cc_final: 0.7865 (tp-100) REVERT: A 436 LEU cc_start: 0.8880 (mt) cc_final: 0.8670 (mt) REVERT: A 720 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7744 (tp-100) REVERT: A 721 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7818 (mtt180) outliers start: 14 outliers final: 8 residues processed: 91 average time/residue: 0.4271 time to fit residues: 41.4183 Evaluate side-chains 91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET 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 578 LYS Chi-restraints excluded: chain A residue 737 VAL 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: 3.9990 chunk 39 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121985 restraints weight = 7361.919| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.75 r_work: 0.3167 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6487 Z= 0.144 Angle : 0.588 7.965 8911 Z= 0.331 Chirality : 0.044 0.214 994 Planarity : 0.004 0.039 1020 Dihedral : 15.649 142.973 1109 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 1.81 % Allowed : 18.23 % Favored : 79.97 % 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: -0.55 (0.32), residues: 686 helix: 0.85 (0.35), residues: 237 sheet: 0.42 (0.44), residues: 145 loop : -1.79 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.016 0.001 TYR A 719 PHE 0.020 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 0.00299 / 0.14 ( 6487) covalent geometry : angle 0.58778 / 0.33 ( 8911) hydrogen bonds : bond 0.03919 / 2.51 ( 246) hydrogen bonds : angle 4.44735 / 3.22 ( 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 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7546 (m-70) cc_final: 0.7334 (m90) REVERT: A 427 SER cc_start: 0.7446 (OUTLIER) cc_final: 0.6997 (p) REVERT: A 435 GLN cc_start: 0.8215 (tt0) cc_final: 0.7802 (tp-100) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.3928 time to fit residues: 38.8740 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET 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: 3.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126982 restraints weight = 7097.271| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.70 r_work: 0.3269 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.154 Angle : 0.604 9.530 8911 Z= 0.336 Chirality : 0.045 0.220 994 Planarity : 0.004 0.040 1020 Dihedral : 15.616 142.113 1109 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 1.64 % Allowed : 18.88 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.32), residues: 686 helix: 0.88 (0.35), residues: 234 sheet: 0.43 (0.44), residues: 145 loop : -1.78 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.015 0.001 TYR A 719 PHE 0.021 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 0.00325 / 0.15 ( 6487) covalent geometry : angle 0.60414 / 0.34 ( 8911) hydrogen bonds : bond 0.04026 / 2.58 ( 246) hydrogen bonds : angle 4.46685 / 3.23 ( 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 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7541 (m-70) cc_final: 0.7332 (m90) REVERT: A 427 SER cc_start: 0.7412 (t) cc_final: 0.7006 (p) REVERT: A 435 GLN cc_start: 0.8188 (tt0) cc_final: 0.7805 (tp-100) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.4186 time to fit residues: 40.3361 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 73 MET 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 0.0070 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128823 restraints weight = 7165.610| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.72 r_work: 0.3301 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6487 Z= 0.127 Angle : 0.579 9.991 8911 Z= 0.323 Chirality : 0.044 0.204 994 Planarity : 0.003 0.039 1020 Dihedral : 15.501 140.928 1109 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.25 % Favored : 94.31 % Rotamer: Outliers : 1.97 % Allowed : 18.88 % Favored : 79.15 % 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: -0.56 (0.32), residues: 686 helix: 0.85 (0.35), residues: 236 sheet: 0.45 (0.44), residues: 140 loop : -1.77 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.015 0.001 TYR A 719 PHE 0.020 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 0.00249 / 0.13 ( 6487) covalent geometry : angle 0.57920 / 0.32 ( 8911) hydrogen bonds : bond 0.03563 / 2.28 ( 246) hydrogen bonds : angle 4.39620 / 3.18 ( 679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.30 seconds wall clock time: 36 minutes 1.90 seconds (2161.90 seconds total)