Starting phenix.real_space_refine on Wed Aug 5 17:12:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhv_38355/08_2026/8xhv_38355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhv_38355/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhv_38355/08_2026/8xhv_38355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhv_38355/08_2026/8xhv_38355.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhv_38355/08_2026/8xhv_38355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhv_38355/08_2026/8xhv_38355.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 20 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 19} Link IDs: {None: 19} 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: 1.33, per 1000 atoms: 0.21 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 353.2 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: 0.52 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: 1.04 Time building geometry restraints manager: 0.62 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 2.320 nonbonded pdb=" OP1 A B 3 " pdb="MN MN A 801 " model vdw 1.857 2.320 nonbonded pdb=" C VAL A 737 " pdb="MN MN A 801 " model vdw 1.982 2.550 nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 2.066 2.320 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- 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 : 0.590 8.661 8654 Z= 0.361 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 0.58980 / 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 : 0.261 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: 0.7136 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.5494 time to fit residues: 71.9007 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 138 ASN A 259 GLN A 541 ASN A 571 ASN A 663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144214 restraints weight = 6480.100| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.49 r_work: 0.3308 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1401 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= 0.140 Angle : 0.566 7.494 8654 Z= 0.317 Chirality : 0.044 0.150 965 Planarity : 0.004 0.040 1047 Dihedral : 12.438 76.912 943 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.72 % Allowed : 10.94 % Favored : 87.34 % 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: 0.01 (0.31), residues: 715 helix: 1.39 (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 0.007 0.000 ARG A 291 TYR 0.019 0.001 TYR A 242 PHE 0.022 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 0.00303 / 0.14 ( 6348) covalent geometry : angle 0.56645 / 0.32 ( 8654) hydrogen bonds : bond 0.04827 / 3.08 ( 248) hydrogen bonds : angle 5.33696 / 3.88 ( 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.161 Fit side-chains REVERT: A 159 THR cc_start: 0.7146 (p) cc_final: 0.6784 (t) REVERT: A 183 GLN cc_start: 0.5860 (mm-40) cc_final: 0.5203 (mt0) REVERT: A 322 ASP cc_start: 0.7594 (m-30) cc_final: 0.7235 (m-30) REVERT: A 435 GLN cc_start: 0.6986 (pt0) cc_final: 0.6522 (mp10) REVERT: A 439 GLN cc_start: 0.7609 (pt0) cc_final: 0.6983 (mt0) REVERT: A 600 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7676 (ptp-170) REVERT: A 624 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8332 (mtpp) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 0.4860 time to fit residues: 52.6439 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 : 0.220 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN A 548 HIS 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 = 0.4088 r_free = 0.4088 target = 0.186556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143276 restraints weight = 6502.108| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.32 r_work: 0.3293 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6348 Z= 0.209 Angle : 0.636 8.304 8654 Z= 0.350 Chirality : 0.047 0.156 965 Planarity : 0.004 0.038 1047 Dihedral : 12.528 75.679 943 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.75 % Allowed : 13.75 % Favored : 82.50 % 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: -0.22 (0.31), residues: 715 helix: 1.09 (0.33), residues: 252 sheet: 0.42 (0.41), residues: 162 loop : -1.58 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.024 0.002 TYR A 242 PHE 0.018 0.002 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.006 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 6348) covalent geometry : angle 0.63647 / 0.35 ( 8654) hydrogen bonds : bond 0.05543 / 3.55 ( 248) hydrogen bonds : angle 5.14072 / 3.73 ( 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: 24 poor density : 85 time to evaluate : 0.245 Fit side-chains REVERT: A 12 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 38 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6333 (p90) REVERT: A 61 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: A 183 GLN cc_start: 0.5927 (mm-40) cc_final: 0.5405 (mt0) REVERT: A 278 CYS cc_start: 0.8502 (t) cc_final: 0.8267 (m) REVERT: A 435 GLN cc_start: 0.7325 (pt0) cc_final: 0.6861 (mp10) REVERT: A 600 ARG cc_start: 0.8029 (ptp-110) cc_final: 0.7806 (ptp-170) outliers start: 24 outliers final: 10 residues processed: 98 average time/residue: 0.4882 time to fit residues: 50.6624 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU 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: 1.9990 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 461 GLN A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.186462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139932 restraints weight = 6538.665| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.63 r_work: 0.3281 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6348 Z= 0.199 Angle : 0.628 9.493 8654 Z= 0.345 Chirality : 0.046 0.150 965 Planarity : 0.004 0.038 1047 Dihedral : 12.605 76.407 943 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.06 % Allowed : 17.19 % Favored : 78.75 % 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: -0.26 (0.31), residues: 715 helix: 1.02 (0.33), residues: 252 sheet: 0.49 (0.42), residues: 158 loop : -1.59 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.026 0.002 TYR A 242 PHE 0.020 0.002 PHE A 401 TRP 0.012 0.002 TRP A 282 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 6348) covalent geometry : angle 0.62844 / 0.35 ( 8654) hydrogen bonds : bond 0.05206 / 3.32 ( 248) hydrogen bonds : angle 5.03502 / 3.64 ( 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 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.217 Fit side-chains REVERT: A 12 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 38 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 61 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: A 183 GLN cc_start: 0.5934 (mm-40) cc_final: 0.5403 (mt0) REVERT: A 322 ASP cc_start: 0.7717 (m-30) cc_final: 0.7386 (m-30) REVERT: A 600 ARG cc_start: 0.8032 (ptp-110) cc_final: 0.7826 (ptp-170) outliers start: 26 outliers final: 13 residues processed: 92 average time/residue: 0.5455 time to fit residues: 52.7359 Evaluate side-chains 89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 314 THR 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 453 THR Chi-restraints excluded: chain A residue 485 ASP 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=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: 9.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 chunk 52 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.186653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130934 restraints weight = 6653.678| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.21 r_work: 0.3259 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6348 Z= 0.175 Angle : 0.595 9.089 8654 Z= 0.328 Chirality : 0.045 0.184 965 Planarity : 0.004 0.037 1047 Dihedral : 12.600 77.159 943 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.06 % Allowed : 17.81 % Favored : 78.12 % 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: 252 sheet: 0.52 (0.42), residues: 155 loop : -1.62 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.024 0.002 TYR A 242 PHE 0.019 0.002 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 6348) covalent geometry : angle 0.59543 / 0.33 ( 8654) hydrogen bonds : bond 0.04883 / 3.11 ( 248) hydrogen bonds : angle 4.91808 / 3.56 ( 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 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.174 Fit side-chains REVERT: A 12 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 38 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6402 (p90) REVERT: A 183 GLN cc_start: 0.5941 (mm-40) cc_final: 0.5419 (mt0) REVERT: A 322 ASP cc_start: 0.7687 (m-30) cc_final: 0.7307 (m-30) REVERT: A 435 GLN cc_start: 0.7386 (pt0) cc_final: 0.6860 (mp10) REVERT: A 509 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 600 ARG cc_start: 0.8037 (ptp-110) cc_final: 0.7801 (ptp-170) outliers start: 26 outliers final: 13 residues processed: 94 average time/residue: 0.4762 time to fit residues: 47.1906 Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 233 VAL 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 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 453 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 635 SER Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN 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: 4.9990 chunk 65 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.188836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142650 restraints weight = 6535.773| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.50 r_work: 0.3335 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6348 Z= 0.128 Angle : 0.554 10.109 8654 Z= 0.304 Chirality : 0.043 0.178 965 Planarity : 0.003 0.037 1047 Dihedral : 12.542 78.642 943 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.22 % Allowed : 19.06 % Favored : 76.72 % 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: -0.21 (0.31), residues: 715 helix: 1.04 (0.33), residues: 254 sheet: 0.56 (0.42), residues: 155 loop : -1.56 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.019 0.001 TYR A 242 PHE 0.019 0.001 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6348) covalent geometry : angle 0.55389 / 0.30 ( 8654) hydrogen bonds : bond 0.04079 / 2.64 ( 248) hydrogen bonds : angle 4.77089 / 3.46 ( 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 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.134 Fit side-chains REVERT: A 12 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 38 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6297 (p90) REVERT: A 183 GLN cc_start: 0.5878 (mm-40) cc_final: 0.5395 (mt0) REVERT: A 322 ASP cc_start: 0.7664 (m-30) cc_final: 0.7251 (m-30) REVERT: A 432 ARG cc_start: 0.6551 (mtm180) cc_final: 0.6337 (mtm180) REVERT: A 435 GLN cc_start: 0.7335 (pt0) cc_final: 0.6828 (mp10) REVERT: A 600 ARG cc_start: 0.8013 (ptp-110) cc_final: 0.7767 (ptp-170) outliers start: 27 outliers final: 13 residues processed: 97 average time/residue: 0.4448 time to fit residues: 45.4364 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 114 HIS Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 233 VAL 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 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 635 SER Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 364 GLN A 461 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141292 restraints weight = 6565.604| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.27 r_work: 0.3299 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6348 Z= 0.188 Angle : 0.611 9.148 8654 Z= 0.334 Chirality : 0.045 0.172 965 Planarity : 0.004 0.038 1047 Dihedral : 12.639 77.911 943 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.91 % Allowed : 19.69 % Favored : 76.41 % 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: -0.27 (0.31), residues: 715 helix: 0.97 (0.33), residues: 253 sheet: 0.41 (0.42), residues: 161 loop : -1.53 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.022 0.002 TYR A 242 PHE 0.019 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 0.00441 / 0.19 ( 6348) covalent geometry : angle 0.61054 / 0.33 ( 8654) hydrogen bonds : bond 0.04937 / 3.14 ( 248) hydrogen bonds : angle 4.83159 / 3.49 ( 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 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.199 Fit side-chains REVERT: A 12 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: A 38 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 183 GLN cc_start: 0.5985 (mm-40) cc_final: 0.5529 (mt0) REVERT: A 322 ASP cc_start: 0.7693 (m-30) cc_final: 0.7286 (m-30) REVERT: A 435 GLN cc_start: 0.7438 (pt0) cc_final: 0.7004 (mp10) REVERT: A 600 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7798 (ptp-170) outliers start: 25 outliers final: 16 residues processed: 95 average time/residue: 0.4179 time to fit residues: 41.9956 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain A residue 233 VAL 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 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.187631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140722 restraints weight = 6578.578| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.70 r_work: 0.3301 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2663 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= 0.153 Angle : 0.573 8.174 8654 Z= 0.315 Chirality : 0.044 0.162 965 Planarity : 0.003 0.037 1047 Dihedral : 12.640 78.800 943 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.06 % Allowed : 20.00 % Favored : 75.94 % 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: -0.21 (0.31), residues: 715 helix: 1.07 (0.33), residues: 251 sheet: 0.55 (0.42), residues: 155 loop : -1.55 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.020 0.001 TYR A 242 PHE 0.020 0.002 PHE A 401 TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6348) covalent geometry : angle 0.57254 / 0.31 ( 8654) hydrogen bonds : bond 0.04469 / 2.86 ( 248) hydrogen bonds : angle 4.75670 / 3.44 ( 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 : 0.192 Fit side-chains REVERT: A 12 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 38 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6365 (p90) REVERT: A 44 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.6088 (mm-40) REVERT: A 183 GLN cc_start: 0.5906 (mm-40) cc_final: 0.5445 (mt0) REVERT: A 203 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 322 ASP cc_start: 0.7631 (m-30) cc_final: 0.7240 (m-30) REVERT: A 509 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7420 (mt) REVERT: A 600 ARG cc_start: 0.8035 (ptp-110) cc_final: 0.7786 (ptp-170) REVERT: A 692 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8481 (mp) outliers start: 26 outliers final: 13 residues processed: 102 average time/residue: 0.4628 time to fit residues: 49.7708 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 233 VAL 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 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 692 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 435 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 = 0.4110 r_free = 0.4110 target = 0.188815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134883 restraints weight = 6560.583| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.05 r_work: 0.3318 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2722 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= 0.123 Angle : 0.547 8.849 8654 Z= 0.302 Chirality : 0.043 0.159 965 Planarity : 0.003 0.036 1047 Dihedral : 12.602 80.037 943 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.44 % Allowed : 21.09 % 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: -0.09 (0.31), residues: 715 helix: 1.27 (0.33), residues: 246 sheet: 0.58 (0.42), residues: 155 loop : -1.51 (0.32), residues: 314 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 0.020 0.001 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6348) covalent geometry : angle 0.54734 / 0.30 ( 8654) hydrogen bonds : bond 0.03900 / 2.50 ( 248) hydrogen bonds : angle 4.62488 / 3.35 ( 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 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.230 Fit side-chains REVERT: A 12 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 38 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6336 (p90) REVERT: A 41 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7605 (tpp-160) REVERT: A 73 MET cc_start: 0.6733 (mpt) cc_final: 0.6323 (OUTLIER) REVERT: A 183 GLN cc_start: 0.5933 (mm-40) cc_final: 0.5458 (mt0) REVERT: A 203 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7066 (pp) REVERT: A 322 ASP cc_start: 0.7552 (m-30) cc_final: 0.7159 (m-30) REVERT: A 600 ARG cc_start: 0.8018 (ptp-110) cc_final: 0.7776 (ptp-170) outliers start: 22 outliers final: 14 residues processed: 102 average time/residue: 0.4592 time to fit residues: 49.5141 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 176 VAL 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 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 435 GLN A 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133150 restraints weight = 6540.152| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.92 r_work: 0.3353 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6348 Z= 0.114 Angle : 0.541 8.955 8654 Z= 0.298 Chirality : 0.043 0.153 965 Planarity : 0.003 0.036 1047 Dihedral : 12.591 80.725 943 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.81 % Allowed : 21.72 % 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: -0.11 (0.31), residues: 715 helix: 1.30 (0.33), residues: 245 sheet: 0.59 (0.42), residues: 155 loop : -1.57 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.016 0.001 TYR A 242 PHE 0.019 0.001 PHE A 401 TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6348) covalent geometry : angle 0.54120 / 0.30 ( 8654) hydrogen bonds : bond 0.03735 / 2.40 ( 248) hydrogen bonds : angle 4.55446 / 3.30 ( 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 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.226 Fit side-chains REVERT: A 38 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6338 (p90) REVERT: A 67 MET cc_start: 0.6992 (mmp) cc_final: 0.6673 (mmp) REVERT: A 73 MET cc_start: 0.6723 (mpt) cc_final: 0.6271 (pmm) REVERT: A 124 ILE cc_start: 0.7582 (mp) cc_final: 0.7369 (mp) REVERT: A 183 GLN cc_start: 0.5903 (mm-40) cc_final: 0.5405 (mt0) REVERT: A 203 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7059 (pp) REVERT: A 322 ASP cc_start: 0.7480 (m-30) cc_final: 0.7081 (m-30) REVERT: A 414 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: A 600 ARG cc_start: 0.7983 (ptp-110) cc_final: 0.7738 (ptp-170) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.4343 time to fit residues: 44.5199 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 176 VAL 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 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.0370 chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 435 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 = 0.4102 r_free = 0.4102 target = 0.188080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131200 restraints weight = 6489.916| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.90 r_work: 0.3335 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2768 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= 0.147 Angle : 0.578 8.738 8654 Z= 0.317 Chirality : 0.044 0.161 965 Planarity : 0.003 0.035 1047 Dihedral : 12.612 80.325 943 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.12 % Allowed : 21.88 % Favored : 75.00 % 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 are not related in a simple way. whole: -0.14 (0.31), residues: 715 helix: 1.25 (0.33), residues: 246 sheet: 0.58 (0.42), residues: 155 loop : -1.58 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.017 0.001 TYR A 242 PHE 0.013 0.001 PHE A 86 TRP 0.011 0.001 TRP A 282 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6348) covalent geometry : angle 0.57769 / 0.32 ( 8654) hydrogen bonds : bond 0.04210 / 2.68 ( 248) hydrogen bonds : angle 4.58710 / 3.32 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.03 seconds wall clock time: 41 minutes 18.09 seconds (2478.09 seconds total)