Starting phenix.real_space_refine on Wed Feb 12 14:07:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.map" model { file = "/net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d43_27173/02_2025/8d43_27173.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4926 2.51 5 N 1346 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7763 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6952 Classifications: {'peptide': 862} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 801} Chain breaks: 2 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.70 Number of scatterers: 7763 At special positions: 0 Unit cell: (70.62, 88.81, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 35 16.00 O 1454 8.00 N 1346 7.00 C 4926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 112 " distance=2.03 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 97 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 930.8 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 22.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.624A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.799A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.517A pdb=" N GLY A 565 " --> pdb=" O HIS A 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 566 " --> pdb=" O TYR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 571 through 592 removed outlier: 4.340A pdb=" N GLY A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.689A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.875A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 685 through 689 removed outlier: 3.912A pdb=" N LEU A 689 " --> pdb=" O PRO A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.597A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.203A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.113A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.812A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.390A pdb=" N HIS B 29 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.830A pdb=" N MET A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 321 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 645 removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 599 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP A 615 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 601 " --> pdb=" O TRP A 615 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 600 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 463 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TRP A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 465 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.941A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.129A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 916 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 840 through 846 removed outlier: 3.596A pdb=" N TRP A 939 " --> pdb=" O SER A 874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 77 273 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2400 1.33 - 1.46: 1518 1.46 - 1.58: 4014 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7985 Sorted by residual: bond pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.22e-02 6.72e+03 7.99e+00 bond pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 1.525 1.493 0.031 1.28e-02 6.10e+03 5.99e+00 bond pdb=" C CYS B 70 " pdb=" O CYS B 70 " ideal model delta sigma weight residual 1.240 1.214 0.025 1.16e-02 7.43e+03 4.68e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.522 1.506 0.016 8.30e-03 1.45e+04 3.58e+00 bond pdb=" C ARG A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.32e-02 5.74e+03 3.57e+00 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 10547 2.19 - 4.38: 281 4.38 - 6.58: 31 6.58 - 8.77: 11 8.77 - 10.96: 3 Bond angle restraints: 10873 Sorted by residual: angle pdb=" N SER A 506 " pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 108.96 98.00 10.96 1.59e+00 3.96e-01 4.75e+01 angle pdb=" C ARG A 110 " pdb=" N PRO A 111 " pdb=" CA PRO A 111 " ideal model delta sigma weight residual 119.76 113.52 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N ASP B 101 " pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 108.20 97.58 10.62 1.71e+00 3.42e-01 3.86e+01 angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 115.64 108.38 7.26 1.46e+00 4.69e-01 2.48e+01 angle pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta sigma weight residual 110.39 117.49 -7.10 1.61e+00 3.86e-01 1.94e+01 ... (remaining 10868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 4254 24.49 - 48.98: 423 48.98 - 73.47: 62 73.47 - 97.95: 22 97.95 - 122.44: 8 Dihedral angle restraints: 4769 sinusoidal: 1995 harmonic: 2774 Sorted by residual: dihedral pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual 122.80 136.80 -14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C TRP A 503 " pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual -122.60 -133.76 11.16 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" O2 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" C3 MAN C 4 " pdb=" O3 MAN C 4 " ideal model delta sinusoidal sigma weight residual -57.63 64.81 -122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1067 0.102 - 0.205: 80 0.205 - 0.307: 6 0.307 - 0.410: 1 0.410 - 0.512: 1 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.22e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.14e+01 ... (remaining 1152 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.143 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" C7 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 503 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 504 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 826 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 827 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 827 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 827 " 0.032 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 1750 2.78 - 3.49: 10223 3.49 - 4.19: 20876 4.19 - 4.90: 35979 Nonbonded interactions: 68829 Sorted by model distance: nonbonded pdb=" OD2 ASP B 57 " pdb="CA CA B 602 " model vdw 1.371 2.510 nonbonded pdb=" OE2 GLU B 105 " pdb="CA CA B 601 " model vdw 2.091 2.510 nonbonded pdb=" OD1 ASP B 94 " pdb="CA CA B 601 " model vdw 2.112 2.510 nonbonded pdb=" OD1 ASP B 53 " pdb="CA CA B 602 " model vdw 2.177 2.510 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.194 2.510 ... (remaining 68824 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7985 Z= 0.280 Angle : 0.842 10.960 10873 Z= 0.482 Chirality : 0.057 0.512 1155 Planarity : 0.007 0.119 1426 Dihedral : 19.690 122.443 2981 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.48 % Allowed : 26.82 % Favored : 67.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 954 helix: -1.16 (0.40), residues: 160 sheet: -0.25 (0.33), residues: 223 loop : -1.24 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 503 HIS 0.008 0.001 HIS A 432 PHE 0.016 0.002 PHE A 101 TYR 0.011 0.001 TYR A 287 ARG 0.009 0.001 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.2636 (ttp80) cc_final: 0.2126 (tpm170) REVERT: A 310 ASP cc_start: 0.0472 (OUTLIER) cc_final: 0.0269 (m-30) REVERT: A 446 PHE cc_start: -0.0472 (m-80) cc_final: -0.1924 (m-80) REVERT: A 635 SER cc_start: -0.0488 (OUTLIER) cc_final: -0.0979 (t) REVERT: A 708 LEU cc_start: -0.1898 (OUTLIER) cc_final: -0.2332 (mp) REVERT: A 781 SER cc_start: -0.2229 (OUTLIER) cc_final: -0.3649 (t) REVERT: A 814 MET cc_start: 0.1756 (mmt) cc_final: -0.0771 (tpp) outliers start: 46 outliers final: 13 residues processed: 110 average time/residue: 0.8847 time to fit residues: 105.8192 Evaluate side-chains 53 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A 732 GLN A 785 HIS A 919 HIS A 934 ASN A 942 HIS B 27 ASN B 28 HIS B 29 HIS B 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.212581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.193822 restraints weight = 8865.360| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.67 r_work: 0.4126 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0747 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 7985 Z= 0.339 Angle : 0.882 15.943 10873 Z= 0.439 Chirality : 0.053 0.207 1155 Planarity : 0.008 0.082 1426 Dihedral : 10.151 79.858 1170 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.22 % Allowed : 22.41 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.27), residues: 954 helix: -1.06 (0.35), residues: 168 sheet: -0.45 (0.32), residues: 239 loop : -1.18 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 315 HIS 0.013 0.003 HIS A 572 PHE 0.020 0.003 PHE A 845 TYR 0.023 0.003 TYR A 438 ARG 0.014 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 46 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: -0.1085 (OUTLIER) cc_final: -0.1444 (tp) REVERT: A 259 ILE cc_start: 0.2114 (OUTLIER) cc_final: 0.0870 (mp) REVERT: A 591 SER cc_start: -0.2093 (OUTLIER) cc_final: -0.2533 (t) REVERT: A 615 TRP cc_start: 0.0487 (OUTLIER) cc_final: -0.0184 (p90) REVERT: A 635 SER cc_start: 0.1271 (OUTLIER) cc_final: 0.0213 (t) REVERT: A 656 GLU cc_start: 0.0308 (OUTLIER) cc_final: -0.2326 (mm-30) REVERT: A 699 ASP cc_start: -0.0325 (OUTLIER) cc_final: -0.0597 (t70) REVERT: A 745 GLN cc_start: -0.0783 (OUTLIER) cc_final: -0.1527 (mt0) REVERT: A 814 MET cc_start: 0.1650 (mmt) cc_final: -0.2182 (tpp) REVERT: A 880 GLU cc_start: -0.0634 (OUTLIER) cc_final: -0.0864 (pt0) outliers start: 69 outliers final: 21 residues processed: 107 average time/residue: 1.0174 time to fit residues: 117.5435 Evaluate side-chains 72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.0370 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN A 676 HIS A 785 HIS B 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.222621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.203494 restraints weight = 8952.173| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 1.80 r_work: 0.4209 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4099 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0878 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7985 Z= 0.229 Angle : 0.688 9.815 10873 Z= 0.339 Chirality : 0.046 0.182 1155 Planarity : 0.006 0.056 1426 Dihedral : 8.035 85.401 1153 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.53 % Allowed : 25.27 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.26), residues: 954 helix: -0.74 (0.35), residues: 165 sheet: -0.54 (0.33), residues: 234 loop : -1.16 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 687 HIS 0.008 0.002 HIS A 572 PHE 0.019 0.002 PHE A 46 TYR 0.015 0.002 TYR A 669 ARG 0.011 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 40 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ILE cc_start: 0.2240 (pt) cc_final: 0.1201 (mt) REVERT: A 615 TRP cc_start: 0.0015 (OUTLIER) cc_final: -0.0300 (p90) REVERT: A 635 SER cc_start: 0.1155 (OUTLIER) cc_final: 0.0169 (t) REVERT: A 656 GLU cc_start: 0.0674 (OUTLIER) cc_final: -0.1129 (tm-30) REVERT: A 699 ASP cc_start: -0.0658 (OUTLIER) cc_final: -0.0880 (t70) outliers start: 38 outliers final: 16 residues processed: 73 average time/residue: 0.8902 time to fit residues: 71.1282 Evaluate side-chains 56 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.236641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.220365 restraints weight = 8991.331| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 1.67 r_work: 0.4365 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1229 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7985 Z= 0.245 Angle : 0.745 17.278 10873 Z= 0.362 Chirality : 0.047 0.203 1155 Planarity : 0.006 0.059 1426 Dihedral : 7.551 89.772 1152 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 3.93 % Allowed : 27.41 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.26), residues: 954 helix: -0.68 (0.36), residues: 165 sheet: -0.42 (0.34), residues: 235 loop : -1.20 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 355 HIS 0.045 0.002 HIS B 29 PHE 0.020 0.002 PHE B 30 TYR 0.020 0.002 TYR B 86 ARG 0.012 0.001 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 46 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.1853 (OUTLIER) cc_final: 0.1569 (tt) REVERT: A 142 MET cc_start: 0.2095 (mpp) cc_final: 0.0101 (tpp) REVERT: A 259 ILE cc_start: 0.2500 (OUTLIER) cc_final: 0.2077 (pp) REVERT: A 347 GLU cc_start: 0.4495 (mm-30) cc_final: 0.3739 (pt0) REVERT: A 615 TRP cc_start: 0.0106 (OUTLIER) cc_final: -0.0559 (p90) REVERT: A 635 SER cc_start: 0.1653 (OUTLIER) cc_final: 0.0615 (m) REVERT: A 712 TYR cc_start: 0.0677 (OUTLIER) cc_final: 0.0122 (t80) outliers start: 33 outliers final: 15 residues processed: 73 average time/residue: 0.8286 time to fit residues: 66.6800 Evaluate side-chains 59 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 882 HIS Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.245449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.229105 restraints weight = 8986.427| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 1.67 r_work: 0.4454 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4344 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1376 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7985 Z= 0.217 Angle : 0.717 15.233 10873 Z= 0.347 Chirality : 0.046 0.212 1155 Planarity : 0.006 0.058 1426 Dihedral : 7.053 81.826 1152 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.17 % Allowed : 28.61 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.27), residues: 954 helix: -0.63 (0.37), residues: 166 sheet: -0.40 (0.34), residues: 238 loop : -1.31 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 322 HIS 0.028 0.002 HIS A 882 PHE 0.022 0.002 PHE A 611 TYR 0.017 0.002 TYR A 746 ARG 0.007 0.001 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.3742 (t) cc_final: 0.3391 (t) REVERT: A 74 LEU cc_start: 0.1940 (OUTLIER) cc_final: 0.1629 (tt) REVERT: A 142 MET cc_start: 0.2081 (mpp) cc_final: 0.0090 (tpp) REVERT: A 250 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5029 (pp) REVERT: A 259 ILE cc_start: 0.2753 (OUTLIER) cc_final: 0.2389 (pp) REVERT: A 347 GLU cc_start: 0.4565 (mm-30) cc_final: 0.4053 (pt0) REVERT: A 594 MET cc_start: 0.0898 (mmm) cc_final: 0.0627 (pmm) REVERT: A 615 TRP cc_start: -0.0083 (OUTLIER) cc_final: -0.0577 (p90) REVERT: A 635 SER cc_start: 0.1802 (OUTLIER) cc_final: 0.0943 (m) REVERT: A 712 TYR cc_start: 0.0710 (OUTLIER) cc_final: 0.0137 (t80) REVERT: A 823 MET cc_start: 0.3943 (tmt) cc_final: 0.3653 (tmt) outliers start: 35 outliers final: 15 residues processed: 76 average time/residue: 0.8963 time to fit residues: 74.4406 Evaluate side-chains 61 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 882 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 68 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 855 GLN A 882 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.253860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.237424 restraints weight = 9072.510| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 1.68 r_work: 0.4539 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4451 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1729 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7985 Z= 0.225 Angle : 0.728 14.211 10873 Z= 0.355 Chirality : 0.047 0.222 1155 Planarity : 0.006 0.059 1426 Dihedral : 6.621 74.076 1150 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.01 % Allowed : 26.94 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.27), residues: 954 helix: -0.60 (0.38), residues: 167 sheet: -0.31 (0.34), residues: 229 loop : -1.39 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 521 HIS 0.033 0.002 HIS A 882 PHE 0.016 0.002 PHE A 611 TYR 0.021 0.002 TYR A 578 ARG 0.011 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.3158 (OUTLIER) cc_final: 0.1984 (m) REVERT: A 242 MET cc_start: -0.0144 (OUTLIER) cc_final: -0.2165 (pmm) REVERT: A 250 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5296 (pp) REVERT: A 259 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2672 (pp) REVERT: A 543 MET cc_start: 0.2478 (mtt) cc_final: 0.1614 (tpp) REVERT: A 615 TRP cc_start: -0.0649 (OUTLIER) cc_final: -0.1075 (p90) REVERT: A 712 TYR cc_start: 0.0768 (OUTLIER) cc_final: 0.0137 (t80) outliers start: 42 outliers final: 19 residues processed: 83 average time/residue: 0.8802 time to fit residues: 79.6789 Evaluate side-chains 68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 882 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.260146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.245033 restraints weight = 9360.438| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 1.60 r_work: 0.4616 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4515 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1938 moved from start: 0.8232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7985 Z= 0.218 Angle : 0.713 12.857 10873 Z= 0.355 Chirality : 0.046 0.168 1155 Planarity : 0.006 0.059 1426 Dihedral : 6.528 67.206 1150 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.93 % Allowed : 28.25 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 954 helix: -0.68 (0.37), residues: 168 sheet: -0.30 (0.34), residues: 230 loop : -1.46 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 322 HIS 0.034 0.002 HIS A 882 PHE 0.017 0.002 PHE A 46 TYR 0.022 0.002 TYR A 60 ARG 0.006 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.3051 (mpp) cc_final: 0.0927 (tpt) REVERT: A 259 ILE cc_start: 0.3424 (OUTLIER) cc_final: 0.2959 (pp) REVERT: A 615 TRP cc_start: -0.0390 (OUTLIER) cc_final: -0.0807 (p90) REVERT: A 712 TYR cc_start: 0.0745 (OUTLIER) cc_final: 0.0151 (t80) REVERT: A 823 MET cc_start: 0.4170 (tmt) cc_final: 0.3884 (tmt) REVERT: A 912 GLU cc_start: 0.1246 (OUTLIER) cc_final: 0.0145 (pm20) outliers start: 33 outliers final: 17 residues processed: 73 average time/residue: 0.7157 time to fit residues: 58.6660 Evaluate side-chains 63 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS A 841 GLN A 882 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.272395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.257547 restraints weight = 9434.053| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 1.62 r_work: 0.4696 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4606 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2356 moved from start: 0.9525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7985 Z= 0.252 Angle : 0.741 14.411 10873 Z= 0.368 Chirality : 0.048 0.202 1155 Planarity : 0.007 0.061 1426 Dihedral : 6.268 57.860 1150 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.58 % Allowed : 28.37 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 954 helix: -0.78 (0.38), residues: 168 sheet: -0.42 (0.34), residues: 233 loop : -1.56 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 730 HIS 0.011 0.002 HIS A 882 PHE 0.020 0.002 PHE A 611 TYR 0.046 0.003 TYR B 86 ARG 0.020 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5583 (tt0) REVERT: A 142 MET cc_start: 0.3622 (OUTLIER) cc_final: 0.1372 (tpt) REVERT: A 259 ILE cc_start: 0.3727 (OUTLIER) cc_final: 0.3329 (mp) REVERT: A 615 TRP cc_start: -0.0641 (OUTLIER) cc_final: -0.0962 (p90) REVERT: A 699 ASP cc_start: 0.0107 (OUTLIER) cc_final: -0.0141 (OUTLIER) REVERT: A 712 TYR cc_start: 0.1102 (OUTLIER) cc_final: 0.0373 (t80) outliers start: 30 outliers final: 16 residues processed: 80 average time/residue: 0.7676 time to fit residues: 67.8419 Evaluate side-chains 70 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 0.0030 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 308 HIS ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN A 783 GLN A 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.273221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.259716 restraints weight = 9909.062| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 1.49 r_work: 0.4677 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4589 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3089 moved from start: 1.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7985 Z= 0.349 Angle : 0.879 15.149 10873 Z= 0.447 Chirality : 0.053 0.281 1155 Planarity : 0.008 0.085 1426 Dihedral : 6.503 52.020 1149 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.62 % Allowed : 30.39 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.26), residues: 954 helix: -1.36 (0.35), residues: 180 sheet: -0.38 (0.35), residues: 212 loop : -1.77 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 322 HIS 0.010 0.002 HIS A 568 PHE 0.067 0.004 PHE A 101 TYR 0.056 0.003 TYR B 86 ARG 0.014 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.7020 (m-80) cc_final: 0.6759 (m-80) REVERT: A 309 ARG cc_start: 0.6091 (ptp90) cc_final: 0.5406 (ptm160) REVERT: A 615 TRP cc_start: -0.0112 (OUTLIER) cc_final: -0.0799 (p90) REVERT: A 730 TRP cc_start: 0.4177 (p-90) cc_final: 0.3872 (p-90) REVERT: A 823 MET cc_start: 0.3954 (tmt) cc_final: 0.3710 (tmt) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 0.9570 time to fit residues: 87.6950 Evaluate side-chains 65 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 0.0770 chunk 24 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.0060 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN A 772 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.273338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.259143 restraints weight = 9667.721| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 1.52 r_work: 0.4675 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4588 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3097 moved from start: 1.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7985 Z= 0.223 Angle : 0.739 11.710 10873 Z= 0.363 Chirality : 0.047 0.212 1155 Planarity : 0.006 0.058 1426 Dihedral : 5.863 51.523 1146 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.79 % Allowed : 31.82 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.26), residues: 954 helix: -0.85 (0.37), residues: 174 sheet: -0.24 (0.36), residues: 200 loop : -1.71 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 322 HIS 0.008 0.001 HIS A 568 PHE 0.039 0.002 PHE A 101 TYR 0.017 0.002 TYR A 257 ARG 0.007 0.001 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.3971 (mtm) cc_final: 0.2813 (tpp) REVERT: A 259 ILE cc_start: 0.4813 (mt) cc_final: 0.3817 (pp) REVERT: A 309 ARG cc_start: 0.6005 (ptp90) cc_final: 0.5441 (ptm-80) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.8865 time to fit residues: 76.6217 Evaluate side-chains 64 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 23 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 92 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.277200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.262433 restraints weight = 9581.966| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 1.53 r_work: 0.4700 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4614 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3585 moved from start: 1.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7985 Z= 0.266 Angle : 0.799 11.791 10873 Z= 0.399 Chirality : 0.049 0.261 1155 Planarity : 0.007 0.058 1426 Dihedral : 5.933 51.203 1146 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.91 % Allowed : 33.49 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.26), residues: 954 helix: -1.16 (0.35), residues: 174 sheet: -0.07 (0.36), residues: 199 loop : -1.75 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 322 HIS 0.008 0.001 HIS A 568 PHE 0.046 0.003 PHE A 101 TYR 0.026 0.002 TYR A 669 ARG 0.004 0.001 ARG A 805 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.86 seconds wall clock time: 87 minutes 17.61 seconds (5237.61 seconds total)