Starting phenix.real_space_refine on Sat Aug 23 08:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk0_38412/08_2025/8xk0_38412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk0_38412/08_2025/8xk0_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_2025/8xk0_38412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_2025/8xk0_38412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_2025/8xk0_38412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk0_38412/08_2025/8xk0_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-2.0-5787/lib/python3.9/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: 1.77, per 1000 atoms: 0.28 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: 0.59 Conformation dependent library (CDL) restraints added in 330.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.75 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: 1.32 Time building geometry restraints manager: 0.78 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 1.50e-02 4.44e+03 4.71e+00 bond pdb=" P DA B 17 " pdb=" OP2 DA B 17 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" P DT B 16 " pdb=" OP1 DT B 16 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" P DA B 17 " pdb=" OP1 DA B 17 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 8663 1.54 - 3.08: 206 3.08 - 4.61: 29 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=" N VAL A 542 " pdb=" CA VAL A 542 " pdb=" C VAL A 542 " ideal model delta sigma weight residual 109.34 103.16 6.18 2.08e+00 2.31e-01 8.84e+00 angle pdb=" C TYR A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta sigma weight residual 119.84 123.27 -3.43 1.25e+00 6.40e-01 7.51e+00 angle pdb=" C GLN A 731 " pdb=" N THR A 732 " pdb=" CA THR A 732 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 angle pdb=" C4 DT B 16 " pdb=" C5 DT B 16 " pdb=" C7 DT B 16 " ideal model delta sigma weight residual 122.40 118.49 3.91 1.50e+00 4.44e-01 6.79e+00 ... (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 - 0.116: 977 0.116 - 0.232: 14 0.232 - 0.348: 1 0.348 - 0.465: 0 0.465 - 0.581: 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 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.43e+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 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.27e+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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 6487 Z= 0.155 Angle : 0.595 7.691 8911 Z= 0.327 Chirality : 0.049 0.581 994 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 aren 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 covalent geometry : bond 0.00324 ( 6487) covalent geometry : angle 0.59503 ( 8911) hydrogen bonds : bond 0.18410 ( 246) hydrogen bonds : angle 5.86853 ( 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 : 0.238 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: 0.6158 time to fit residues: 67.1378 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 : 0.248 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 259 GLN A 465 HIS A 467 HIS A 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122257 restraints weight = 7301.002| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.93 r_work: 0.3177 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6487 Z= 0.160 Angle : 0.597 8.951 8911 Z= 0.324 Chirality : 0.043 0.165 994 Planarity : 0.004 0.042 1020 Dihedral : 15.679 148.267 1111 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.69 % Favored : 94.02 % Rotamer: Outliers : 1.31 % Allowed : 10.18 % Favored : 88.51 % 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 aren not related in a simple way. whole: -0.66 (0.32), residues: 686 helix: 0.68 (0.35), residues: 237 sheet: 0.13 (0.43), residues: 146 loop : -1.64 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 291 TYR 0.011 0.001 TYR A 130 PHE 0.023 0.002 PHE A 401 TRP 0.004 0.001 TRP A 512 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6487) covalent geometry : angle 0.59706 ( 8911) hydrogen bonds : bond 0.04659 ( 246) hydrogen bonds : angle 4.61074 ( 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 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.257 Fit side-chains REVERT: A 108 HIS cc_start: 0.7560 (m-70) cc_final: 0.7341 (m90) REVERT: A 435 GLN cc_start: 0.8167 (tt0) cc_final: 0.7822 (tp-100) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.4989 time to fit residues: 52.8366 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 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: 0.9980 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 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 = 0.3812 r_free = 0.3812 target = 0.158102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120642 restraints weight = 7276.268| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.93 r_work: 0.3133 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6487 Z= 0.174 Angle : 0.598 8.466 8911 Z= 0.326 Chirality : 0.043 0.165 994 Planarity : 0.004 0.038 1020 Dihedral : 15.633 144.868 1109 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.98 % Favored : 93.73 % Rotamer: Outliers : 1.31 % Allowed : 14.12 % Favored : 84.56 % 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 aren not related in a simple way. whole: -0.64 (0.32), residues: 686 helix: 0.74 (0.35), residues: 237 sheet: 0.34 (0.44), residues: 140 loop : -1.76 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.011 0.001 TYR A 130 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 covalent geometry : bond 0.00399 ( 6487) covalent geometry : angle 0.59799 ( 8911) hydrogen bonds : bond 0.04499 ( 246) hydrogen bonds : angle 4.56624 ( 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 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7600 (m-70) cc_final: 0.7365 (m90) REVERT: A 435 GLN cc_start: 0.8252 (tt0) cc_final: 0.7864 (tp-100) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 0.5060 time to fit residues: 49.8965 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 737 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3813 r_free = 0.3813 target = 0.158279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120914 restraints weight = 7297.902| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.69 r_work: 0.3156 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1544 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= 0.163 Angle : 0.581 7.660 8911 Z= 0.318 Chirality : 0.043 0.168 994 Planarity : 0.004 0.039 1020 Dihedral : 15.541 143.742 1109 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.83 % Favored : 93.88 % Rotamer: Outliers : 2.13 % Allowed : 15.60 % Favored : 82.27 % 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 aren not related in a simple way. whole: -0.58 (0.32), residues: 686 helix: 0.81 (0.35), residues: 237 sheet: 0.20 (0.43), residues: 146 loop : -1.68 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.011 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 covalent geometry : bond 0.00375 ( 6487) covalent geometry : angle 0.58146 ( 8911) hydrogen bonds : bond 0.04172 ( 246) hydrogen bonds : angle 4.49848 ( 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 102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7541 (m-70) cc_final: 0.7330 (m90) REVERT: A 435 GLN cc_start: 0.8214 (tt0) cc_final: 0.7823 (tp-100) REVERT: A 578 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7885 (mmmm) outliers start: 13 outliers final: 5 residues processed: 95 average time/residue: 0.4816 time to fit residues: 48.6759 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 : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 549 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: 0.8980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3920 r_free = 0.3920 target = 0.163847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127881 restraints weight = 7193.931| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.69 r_work: 0.3246 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6487 Z= 0.151 Angle : 0.570 8.317 8911 Z= 0.311 Chirality : 0.043 0.173 994 Planarity : 0.004 0.039 1020 Dihedral : 15.467 141.979 1109 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 2.46 % Allowed : 16.58 % 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 aren not related in a simple way. whole: -0.46 (0.32), residues: 686 helix: 0.96 (0.36), residues: 234 sheet: 0.29 (0.43), residues: 146 loop : -1.64 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.012 0.001 TYR A 719 PHE 0.021 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 covalent geometry : bond 0.00346 ( 6487) covalent geometry : angle 0.56963 ( 8911) hydrogen bonds : bond 0.03941 ( 246) hydrogen bonds : angle 4.44397 ( 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 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7534 (m-70) cc_final: 0.7330 (m90) REVERT: A 435 GLN cc_start: 0.8178 (tt0) cc_final: 0.7824 (tp-100) REVERT: A 721 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7788 (mtt180) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 0.4942 time to fit residues: 51.4184 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 : 0.227 ------------------------------------------------------------------------------- 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 549 LEU Chi-restraints excluded: chain A residue 572 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: 4.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 552 GLN A 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125213 restraints weight = 7160.655| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.70 r_work: 0.3247 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6487 Z= 0.188 Angle : 0.608 8.707 8911 Z= 0.332 Chirality : 0.044 0.167 994 Planarity : 0.004 0.041 1020 Dihedral : 15.606 141.640 1109 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.98 % Favored : 93.59 % Rotamer: Outliers : 2.96 % Allowed : 18.23 % Favored : 78.82 % 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 aren not related in a simple way. whole: -0.59 (0.32), residues: 686 helix: 0.75 (0.35), residues: 239 sheet: 0.21 (0.42), residues: 160 loop : -1.75 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.012 0.001 TYR A 719 PHE 0.022 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 covalent geometry : bond 0.00437 ( 6487) covalent geometry : angle 0.60833 ( 8911) hydrogen bonds : bond 0.04457 ( 246) hydrogen bonds : angle 4.57044 ( 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: 18 poor density : 83 time to evaluate : 0.253 Fit side-chains REVERT: A 40 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7239 (ttt) REVERT: A 435 GLN cc_start: 0.8135 (tt0) cc_final: 0.7776 (tp-100) REVERT: A 562 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6434 (mm-30) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 0.4947 time to fit residues: 50.4927 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 562 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 737 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129568 restraints weight = 7120.508| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.70 r_work: 0.3305 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1810 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= 0.119 Angle : 0.552 7.979 8911 Z= 0.300 Chirality : 0.041 0.164 994 Planarity : 0.003 0.037 1020 Dihedral : 15.236 138.972 1109 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.81 % Favored : 94.75 % Rotamer: Outliers : 2.63 % Allowed : 18.88 % Favored : 78.49 % 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 aren not related in a simple way. whole: -0.38 (0.32), residues: 686 helix: 0.99 (0.35), residues: 236 sheet: 0.39 (0.43), residues: 146 loop : -1.62 (0.33), residues: 304 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 0.020 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 covalent geometry : bond 0.00261 ( 6487) covalent geometry : angle 0.55161 ( 8911) hydrogen bonds : bond 0.03297 ( 246) hydrogen bonds : angle 4.32227 ( 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 104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8083 (tt0) cc_final: 0.7730 (tp-100) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 0.4846 time to fit residues: 51.5808 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3912 r_free = 0.3912 target = 0.163396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126477 restraints weight = 7124.322| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.73 r_work: 0.3270 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6487 Z= 0.160 Angle : 0.595 9.252 8911 Z= 0.322 Chirality : 0.043 0.167 994 Planarity : 0.004 0.039 1020 Dihedral : 15.435 138.060 1109 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 1.81 % Allowed : 19.87 % Favored : 78.33 % 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 aren not related in a simple way. whole: -0.48 (0.32), residues: 686 helix: 0.84 (0.35), residues: 239 sheet: 0.18 (0.41), residues: 166 loop : -1.65 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.014 0.001 TYR A 719 PHE 0.021 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 covalent geometry : bond 0.00369 ( 6487) covalent geometry : angle 0.59511 ( 8911) hydrogen bonds : bond 0.04024 ( 246) hydrogen bonds : angle 4.45044 ( 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: 11 poor density : 86 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8082 (tt0) cc_final: 0.7736 (tp-100) REVERT: A 721 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7714 (mtt180) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.5296 time to fit residues: 51.6093 Evaluate side-chains 91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130851 restraints weight = 7206.420| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.65 r_work: 0.3323 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1931 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= 0.119 Angle : 0.559 9.773 8911 Z= 0.301 Chirality : 0.042 0.172 994 Planarity : 0.003 0.039 1020 Dihedral : 15.154 135.073 1109 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.81 % Favored : 94.75 % Rotamer: Outliers : 1.64 % Allowed : 20.36 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.32), residues: 686 helix: 0.92 (0.35), residues: 236 sheet: 0.25 (0.42), residues: 161 loop : -1.60 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.014 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 covalent geometry : bond 0.00265 ( 6487) covalent geometry : angle 0.55946 ( 8911) hydrogen bonds : bond 0.03282 ( 246) hydrogen bonds : angle 4.32805 ( 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 102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.7967 (tt0) cc_final: 0.7667 (tp-100) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.4671 time to fit residues: 49.2346 Evaluate side-chains 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 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 75 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 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124850 restraints weight = 7113.887| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.72 r_work: 0.3146 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6487 Z= 0.203 Angle : 0.644 10.074 8911 Z= 0.345 Chirality : 0.045 0.198 994 Planarity : 0.004 0.061 1020 Dihedral : 15.570 135.085 1109 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 1.81 % Allowed : 20.36 % Favored : 77.83 % 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 aren not related in a simple way. whole: -0.67 (0.32), residues: 686 helix: 0.66 (0.35), residues: 239 sheet: 0.20 (0.42), residues: 160 loop : -1.79 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 291 TYR 0.016 0.001 TYR A 719 PHE 0.022 0.002 PHE A 319 TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6487) covalent geometry : angle 0.64444 ( 8911) hydrogen bonds : bond 0.04579 ( 246) hydrogen bonds : angle 4.62495 ( 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 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8026 (tt0) cc_final: 0.7703 (tp-100) outliers start: 11 outliers final: 8 residues processed: 93 average time/residue: 0.5062 time to fit residues: 49.9420 Evaluate side-chains 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 75 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 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3938 r_free = 0.3938 target = 0.165950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129240 restraints weight = 7171.599| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.72 r_work: 0.3280 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6487 Z= 0.124 Angle : 0.576 10.394 8911 Z= 0.308 Chirality : 0.042 0.179 994 Planarity : 0.004 0.039 1020 Dihedral : 15.179 132.014 1109 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.25 % Favored : 94.31 % Rotamer: Outliers : 1.48 % Allowed : 20.69 % Favored : 77.83 % 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 aren not related in a simple way. whole: -0.50 (0.32), residues: 686 helix: 0.86 (0.35), residues: 236 sheet: 0.58 (0.44), residues: 140 loop : -1.76 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.014 0.001 TYR A 719 PHE 0.019 0.001 PHE A 319 TRP 0.004 0.001 TRP A 445 HIS 0.009 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6487) covalent geometry : angle 0.57630 ( 8911) hydrogen bonds : bond 0.03350 ( 246) hydrogen bonds : angle 4.38181 ( 679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.11 seconds wall clock time: 42 minutes 54.24 seconds (2574.24 seconds total)