Starting phenix.real_space_refine on Thu Jul 2 23:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2026/8xhv_38355.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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 5813 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 1 7.51 5 P 14 5.49 5 S 29 5.16 5 C 3907 2.51 5 N 1092 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5879 Classifications: {'peptide': 721} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 697} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 19 Ad-hoc single atom residues: {' MN': 1} Classifications: {'water': 19} Link IDs: {None: 18} Chain breaks: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.44, per 1000 atoms: 0.23 Number of scatterers: 6199 At special positions: 0 Unit cell: (73.186, 92.759, 106.375, 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 1 24.99 S 29 16.00 P 14 15.00 O 1156 8.00 N 1092 7.00 C 3907 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: 0.46 Conformation dependent library (CDL) restraints added in 287.8 milliseconds 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 38.4% alpha, 19.6% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.854A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.664A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.922A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.736A pdb=" N PHE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 400' Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 409 removed outlier: 3.519A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.797A pdb=" N GLY A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.845A pdb=" N CYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 4.133A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 613 removed outlier: 4.147A 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 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.912A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (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 9 removed outlier: 6.810A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.926A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 243 removed outlier: 4.116A pdb=" N VAL A 230 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 191 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.576A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A 539 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.583A pdb=" N GLY A 339 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR A 381 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 341 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 452 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A 419 " --> pdb=" O ILE A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 248 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1714 1.33 - 1.45: 1150 1.45 - 1.57: 3407 1.57 - 1.69: 27 1.69 - 1.81: 50 Bond restraints: 6348 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C3' G B 11 " pdb=" C2' G B 11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' A B 17 " pdb=" C2' A B 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 bond pdb=" C1' DT B 16 " pdb=" N1 DT B 16 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.88e+00 bond pdb=" O4' G B 11 " pdb=" C1' G B 11 " ideal model delta sigma weight residual 1.420 1.397 0.023 1.10e-02 8.26e+03 4.55e+00 ... (remaining 6343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8459 1.73 - 3.46: 176 3.46 - 5.20: 13 5.20 - 6.93: 3 6.93 - 8.66: 3 Bond angle restraints: 8654 Sorted by residual: angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " pdb=" O4 DT B 18 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" O4 DT B 9 " pdb=" C4 DT B 9 " pdb=" C5 DT B 9 " ideal model delta sigma weight residual 124.90 122.31 2.59 7.00e-01 2.04e+00 1.37e+01 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3262 16.49 - 32.98: 356 32.98 - 49.47: 86 49.47 - 65.96: 30 65.96 - 82.44: 10 Dihedral angle restraints: 3744 sinusoidal: 1611 harmonic: 2133 Sorted by residual: dihedral pdb=" CA PHE A 319 " pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLY A 544 " pdb=" C GLY A 544 " pdb=" N SER A 545 " pdb=" CA SER A 545 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TYR A 242 " pdb=" C TYR A 242 " pdb=" N ALA A 243 " pdb=" CA ALA A 243 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 885 0.082 - 0.164: 79 0.164 - 0.245: 0 0.245 - 0.327: 0 0.327 - 0.409: 1 Chirality restraints: 965 Sorted by residual: chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ILE A 671 " pdb=" N ILE A 671 " pdb=" C ILE A 671 " pdb=" CB ILE A 671 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU A 734 " pdb=" CB LEU A 734 " pdb=" CD1 LEU A 734 " pdb=" CD2 LEU A 734 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 962 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.020 2.00e-02 2.50e+03 9.11e-03 2.08e+00 pdb=" N1 DT B 1 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 511 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 734 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU A 734 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU A 734 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A 735 " -0.007 2.00e-02 2.50e+03 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 14 2.35 - 2.99: 2948 2.99 - 3.63: 8869 3.63 - 4.26: 14177 4.26 - 4.90: 24028 Nonbonded interactions: 50036 Sorted by model distance: nonbonded pdb=" O VAL A 737 " pdb="MN MN A 801 " model vdw 1.715 3.060 nonbonded pdb=" OP1 A B 3 " pdb="MN MN A 801 " model vdw 1.857 3.060 nonbonded pdb=" C VAL A 737 " pdb="MN MN A 801 " model vdw 1.982 3.290 nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 2.066 3.060 nonbonded pdb=" OH TYR A 37 " pdb=" NH2 ARG A 41 " model vdw 2.230 3.120 ... (remaining 50031 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: 1.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 0.120 6348 Z= 0.206 Angle : 0.589 8.661 8654 Z= 0.360 Chirality : 0.045 0.409 965 Planarity : 0.003 0.032 1047 Dihedral : 15.522 82.445 2366 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % 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: -0.01 (0.31), residues: 715 helix: 1.39 (0.33), residues: 248 sheet: 0.71 (0.46), residues: 123 loop : -1.39 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.019 0.001 TYR A 242 PHE 0.020 0.001 PHE A 351 TRP 0.009 0.001 TRP A 282 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.21 ( 6348) covalent geometry : angle 0.58914 / 0.36 ( 8654) hydrogen bonds : bond 0.12985 / 8.43 ( 248) hydrogen bonds : angle 6.64448 / 4.79 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 159 THR cc_start: 0.7198 (p) cc_final: 0.6997 (t) REVERT: A 322 ASP cc_start: 0.7756 (m-30) cc_final: 0.7534 (m-30) REVERT: A 439 GLN cc_start: 0.7565 (pt0) cc_final: 0.7034 (mt0) REVERT: A 600 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7135 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.5445 time to fit residues: 71.0992 Evaluate side-chains 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 541 ASN A 571 ASN A 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145453 restraints weight = 6452.419| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.29 r_work: 0.3318 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6348 Z= 0.142 Angle : 0.568 7.154 8654 Z= 0.318 Chirality : 0.044 0.149 965 Planarity : 0.004 0.037 1047 Dihedral : 12.478 77.108 943 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.72 % Allowed : 10.62 % Favored : 87.66 % 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: 0.01 (0.31), residues: 715 helix: 1.40 (0.33), residues: 254 sheet: 0.53 (0.42), residues: 162 loop : -1.55 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 291 TYR 0.020 0.001 TYR A 242 PHE 0.021 0.002 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6348) covalent geometry : angle 0.56786 / 0.32 ( 8654) hydrogen bonds : bond 0.04897 / 3.12 ( 248) hydrogen bonds : angle 5.34707 / 3.89 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.198 Fit side-chains REVERT: A 159 THR cc_start: 0.7241 (p) cc_final: 0.6875 (t) REVERT: A 183 GLN cc_start: 0.5845 (mm-40) cc_final: 0.5178 (mt0) REVERT: A 322 ASP cc_start: 0.7661 (m-30) cc_final: 0.7249 (m-30) REVERT: A 435 GLN cc_start: 0.7079 (pt0) cc_final: 0.6567 (mp10) REVERT: A 439 GLN cc_start: 0.7602 (pt0) cc_final: 0.6981 (mt0) REVERT: A 600 ARG cc_start: 0.7969 (ptp-110) cc_final: 0.7768 (ptp-170) REVERT: A 624 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8354 (mtpp) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.4956 time to fit residues: 54.1259 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 635 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 HIS A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134845 restraints weight = 6525.921| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.84 r_work: 0.3310 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6348 Z= 0.229 Angle : 0.655 7.858 8654 Z= 0.358 Chirality : 0.047 0.153 965 Planarity : 0.004 0.039 1047 Dihedral : 12.552 75.478 943 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.91 % Allowed : 13.75 % Favored : 82.34 % 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: -0.28 (0.31), residues: 715 helix: 1.03 (0.33), residues: 253 sheet: 0.41 (0.41), residues: 162 loop : -1.61 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.025 0.002 TYR A 242 PHE 0.019 0.002 PHE A 86 TRP 0.011 0.002 TRP A 282 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 6348) covalent geometry : angle 0.65534 / 0.36 ( 8654) hydrogen bonds : bond 0.05782 / 3.68 ( 248) hydrogen bonds : angle 5.21851 / 3.78 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.201 Fit side-chains REVERT: A 12 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: A 38 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6267 (p90) REVERT: A 61 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: A 183 GLN cc_start: 0.5927 (mm-40) cc_final: 0.5331 (mt0) REVERT: A 278 CYS cc_start: 0.8434 (t) cc_final: 0.8194 (m) REVERT: A 414 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: A 435 GLN cc_start: 0.7266 (pt0) cc_final: 0.6817 (mp10) REVERT: A 600 ARG cc_start: 0.8026 (ptp-110) cc_final: 0.7797 (ptp-170) outliers start: 25 outliers final: 11 residues processed: 97 average time/residue: 0.4973 time to fit residues: 50.8786 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141331 restraints weight = 6506.999| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.33 r_work: 0.3319 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6348 Z= 0.148 Angle : 0.564 8.053 8654 Z= 0.312 Chirality : 0.044 0.145 965 Planarity : 0.004 0.038 1047 Dihedral : 12.480 77.032 943 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.12 % Allowed : 16.72 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.31), residues: 715 helix: 1.08 (0.33), residues: 254 sheet: 0.53 (0.41), residues: 160 loop : -1.60 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.022 0.001 TYR A 242 PHE 0.019 0.002 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6348) covalent geometry : angle 0.56384 / 0.31 ( 8654) hydrogen bonds : bond 0.04632 / 2.96 ( 248) hydrogen bonds : angle 4.98617 / 3.61 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.227 Fit side-chains REVERT: A 12 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 38 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6369 (p90) REVERT: A 61 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7889 (m-10) REVERT: A 122 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7702 (tp-100) REVERT: A 183 GLN cc_start: 0.5855 (mm-40) cc_final: 0.5302 (mt0) REVERT: A 322 ASP cc_start: 0.7693 (m-30) cc_final: 0.7304 (m-30) REVERT: A 414 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: A 435 GLN cc_start: 0.7299 (pt0) cc_final: 0.6870 (mp10) REVERT: A 509 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7464 (mt) REVERT: A 600 ARG cc_start: 0.7993 (ptp-110) cc_final: 0.7780 (ptp-170) REVERT: A 734 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6827 (tt) outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.5169 time to fit residues: 49.6249 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS A 259 GLN A 461 GLN A 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128078 restraints weight = 6698.507| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.08 r_work: 0.3196 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 6348 Z= 0.411 Angle : 0.868 9.768 8654 Z= 0.464 Chirality : 0.057 0.220 965 Planarity : 0.006 0.042 1047 Dihedral : 13.000 73.432 943 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.84 % Allowed : 17.81 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.90 (0.30), residues: 715 helix: 0.24 (0.31), residues: 257 sheet: 0.26 (0.41), residues: 160 loop : -1.82 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.040 0.003 TYR A 242 PHE 0.029 0.004 PHE A 86 TRP 0.017 0.003 TRP A 512 HIS 0.011 0.002 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00998 / 0.41 ( 6348) covalent geometry : angle 0.86824 / 0.46 ( 8654) hydrogen bonds : bond 0.07567 / 4.78 ( 248) hydrogen bonds : angle 5.46211 / 3.91 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.251 Fit side-chains REVERT: A 12 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 38 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6801 (p90) REVERT: A 61 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: A 183 GLN cc_start: 0.6120 (mm-40) cc_final: 0.5694 (mt0) REVERT: A 414 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: A 509 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7767 (mt) REVERT: A 583 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: A 600 ARG cc_start: 0.8123 (ptp-110) cc_final: 0.7883 (ptp-170) REVERT: A 734 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6923 (tt) outliers start: 31 outliers final: 15 residues processed: 106 average time/residue: 0.4915 time to fit residues: 54.9823 Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 461 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.188717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144935 restraints weight = 6544.368| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.58 r_work: 0.3314 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6348 Z= 0.132 Angle : 0.572 8.177 8654 Z= 0.316 Chirality : 0.044 0.169 965 Planarity : 0.004 0.039 1047 Dihedral : 12.688 78.204 943 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.59 % Allowed : 20.94 % Favored : 75.47 % 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: -0.43 (0.31), residues: 715 helix: 0.95 (0.33), residues: 252 sheet: 0.28 (0.41), residues: 161 loop : -1.70 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.022 0.001 TYR A 242 PHE 0.021 0.001 PHE A 401 TRP 0.016 0.002 TRP A 282 HIS 0.004 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6348) covalent geometry : angle 0.57183 / 0.32 ( 8654) hydrogen bonds : bond 0.04319 / 2.78 ( 248) hydrogen bonds : angle 4.97493 / 3.60 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.235 Fit side-chains REVERT: A 12 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 38 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6479 (p90) REVERT: A 44 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6228 (mm-40) REVERT: A 183 GLN cc_start: 0.5911 (mm-40) cc_final: 0.5471 (mt0) REVERT: A 435 GLN cc_start: 0.7372 (pt0) cc_final: 0.6863 (mp10) REVERT: A 600 ARG cc_start: 0.8004 (ptp-110) cc_final: 0.7746 (ptp-170) REVERT: A 734 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6977 (tt) outliers start: 23 outliers final: 8 residues processed: 101 average time/residue: 0.4999 time to fit residues: 53.1736 Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.186687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142370 restraints weight = 6562.536| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.73 r_work: 0.3280 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6348 Z= 0.178 Angle : 0.617 9.421 8654 Z= 0.336 Chirality : 0.045 0.178 965 Planarity : 0.004 0.037 1047 Dihedral : 12.695 77.711 943 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.75 % Allowed : 20.94 % Favored : 75.31 % 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: -0.46 (0.31), residues: 715 helix: 0.92 (0.33), residues: 252 sheet: 0.28 (0.41), residues: 161 loop : -1.71 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.024 0.002 TYR A 242 PHE 0.019 0.002 PHE A 401 TRP 0.011 0.001 TRP A 282 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 6348) covalent geometry : angle 0.61735 / 0.34 ( 8654) hydrogen bonds : bond 0.04904 / 3.14 ( 248) hydrogen bonds : angle 4.94489 / 3.57 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.204 Fit side-chains REVERT: A 12 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: A 38 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6398 (p90) REVERT: A 183 GLN cc_start: 0.6019 (mm-40) cc_final: 0.5580 (mt0) REVERT: A 322 ASP cc_start: 0.7768 (m-30) cc_final: 0.7557 (m-30) REVERT: A 414 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: A 435 GLN cc_start: 0.7334 (pt0) cc_final: 0.6904 (mp10) REVERT: A 509 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 600 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7697 (ptp-170) REVERT: A 734 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7036 (tt) outliers start: 24 outliers final: 12 residues processed: 98 average time/residue: 0.4525 time to fit residues: 46.9704 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.188297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143712 restraints weight = 6564.841| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.43 r_work: 0.3308 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6348 Z= 0.134 Angle : 0.569 9.884 8654 Z= 0.311 Chirality : 0.044 0.169 965 Planarity : 0.003 0.037 1047 Dihedral : 12.638 78.998 943 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.06 % Allowed : 21.09 % Favored : 74.84 % 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: -0.36 (0.31), residues: 715 helix: 1.03 (0.33), residues: 251 sheet: 0.34 (0.41), residues: 161 loop : -1.68 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.020 0.001 TYR A 242 PHE 0.020 0.001 PHE A 401 TRP 0.014 0.001 TRP A 282 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6348) covalent geometry : angle 0.56852 / 0.31 ( 8654) hydrogen bonds : bond 0.04211 / 2.71 ( 248) hydrogen bonds : angle 4.80837 / 3.48 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.235 Fit side-chains REVERT: A 12 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: A 38 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6367 (p90) REVERT: A 183 GLN cc_start: 0.5956 (mm-40) cc_final: 0.5492 (mt0) REVERT: A 203 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7071 (pp) REVERT: A 322 ASP cc_start: 0.7655 (m-30) cc_final: 0.7410 (m-30) REVERT: A 414 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 435 GLN cc_start: 0.7296 (pt0) cc_final: 0.6889 (mp10) REVERT: A 600 ARG cc_start: 0.7920 (ptp-110) cc_final: 0.7660 (ptp-170) REVERT: A 734 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7079 (tt) outliers start: 26 outliers final: 13 residues processed: 102 average time/residue: 0.4550 time to fit residues: 49.0974 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133177 restraints weight = 6572.133| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.92 r_work: 0.3350 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6348 Z= 0.117 Angle : 0.554 9.261 8654 Z= 0.302 Chirality : 0.043 0.153 965 Planarity : 0.003 0.037 1047 Dihedral : 12.592 80.059 943 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.97 % Allowed : 22.19 % Favored : 74.84 % 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: -0.30 (0.31), residues: 715 helix: 1.03 (0.33), residues: 251 sheet: 0.54 (0.42), residues: 155 loop : -1.67 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.017 0.001 TYR A 242 PHE 0.019 0.001 PHE A 401 TRP 0.014 0.001 TRP A 282 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6348) covalent geometry : angle 0.55389 / 0.30 ( 8654) hydrogen bonds : bond 0.03822 / 2.47 ( 248) hydrogen bonds : angle 4.66306 / 3.38 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.138 Fit side-chains REVERT: A 38 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6386 (p90) REVERT: A 41 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (tpp-160) REVERT: A 73 MET cc_start: 0.6729 (mpt) cc_final: 0.6317 (OUTLIER) REVERT: A 183 GLN cc_start: 0.5887 (mm-40) cc_final: 0.5406 (mt0) REVERT: A 203 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7080 (pp) REVERT: A 435 GLN cc_start: 0.7331 (pt0) cc_final: 0.6862 (mp10) REVERT: A 600 ARG cc_start: 0.8003 (ptp-110) cc_final: 0.7756 (ptp-170) REVERT: A 734 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7069 (tt) outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.4657 time to fit residues: 49.2730 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131717 restraints weight = 6546.267| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.94 r_work: 0.3332 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6348 Z= 0.144 Angle : 0.586 8.664 8654 Z= 0.319 Chirality : 0.044 0.163 965 Planarity : 0.003 0.036 1047 Dihedral : 12.607 79.873 943 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.97 % Allowed : 22.66 % Favored : 74.38 % 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: -0.31 (0.30), residues: 715 helix: 1.13 (0.33), residues: 245 sheet: 0.56 (0.42), residues: 155 loop : -1.73 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.019 0.001 TYR A 242 PHE 0.012 0.001 PHE A 86 TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6348) covalent geometry : angle 0.58610 / 0.32 ( 8654) hydrogen bonds : bond 0.04217 / 2.70 ( 248) hydrogen bonds : angle 4.68152 / 3.39 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.231 Fit side-chains REVERT: A 38 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6374 (p90) REVERT: A 73 MET cc_start: 0.6788 (mpt) cc_final: 0.6379 (OUTLIER) REVERT: A 124 ILE cc_start: 0.7584 (mp) cc_final: 0.7372 (mp) REVERT: A 183 GLN cc_start: 0.5947 (mm-40) cc_final: 0.5457 (mt0) REVERT: A 203 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7127 (pp) REVERT: A 435 GLN cc_start: 0.7344 (pt0) cc_final: 0.6889 (mp10) REVERT: A 600 ARG cc_start: 0.8000 (ptp-110) cc_final: 0.7750 (ptp-170) REVERT: A 734 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7014 (tt) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.4863 time to fit residues: 50.8879 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.186747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129397 restraints weight = 6475.517| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.91 r_work: 0.3297 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6348 Z= 0.183 Angle : 0.614 9.076 8654 Z= 0.334 Chirality : 0.045 0.180 965 Planarity : 0.004 0.036 1047 Dihedral : 12.646 79.195 943 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.97 % Allowed : 22.81 % Favored : 74.22 % 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: -0.36 (0.31), residues: 715 helix: 1.10 (0.33), residues: 245 sheet: 0.53 (0.42), residues: 155 loop : -1.78 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 88 TYR 0.021 0.002 TYR A 242 PHE 0.023 0.002 PHE A 401 TRP 0.010 0.001 TRP A 282 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 6348) covalent geometry : angle 0.61423 / 0.33 ( 8654) hydrogen bonds : bond 0.04833 / 3.07 ( 248) hydrogen bonds : angle 4.77629 / 3.45 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.40 seconds wall clock time: 43 minutes 51.93 seconds (2631.93 seconds total)