Starting phenix.real_space_refine on Wed Aug 5 03:07:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.map" model { file = "/net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t47_41023/08_2026/8t47_41023.cif" } resolution = 3.16 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= 0.055 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 P 10 5.49 5 S 36 5.16 5 C 5544 2.51 5 N 1290 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8306 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4031 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4031 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {'CO3': 1, 'NAG': 1, 'PIO': 1, 'PLC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {'CO3': 1, 'NAG': 1, 'PIO': 1, 'PLC': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.96, per 1000 atoms: 0.24 Number of scatterers: 8306 At special positions: 0 Unit cell: (119.84, 95.23, 81.32, 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) S 36 16.00 P 10 15.00 O 1426 8.00 N 1290 7.00 C 5544 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 Links applied NAG-ASN " NAG A1005 " - " ASN A 642 " " NAG B1005 " - " ASN B 642 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 414.7 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 77.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 Processing helix chain 'B' and resid 508 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.586A pdb=" N HIS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 594 removed outlier: 3.601A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 623 Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.549A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.547A pdb=" N SER B 731 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 801 removed outlier: 3.772A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 801 " --> pdb=" O VAL B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.598A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.642A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 878 removed outlier: 3.913A pdb=" N LEU B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 594 removed outlier: 3.740A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 703 through 719 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.575A pdb=" N SER A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 776 through 783 Processing helix chain 'A' and resid 784 through 801 removed outlier: 4.030A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 removed outlier: 4.107A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.590A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.659A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.603A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 removed outlier: 3.931A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'B' and resid 462 through 463 removed outlier: 3.527A pdb=" N SER B 725 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'A' and resid 739 through 740 548 hydrogen bonds defined for protein. 1581 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: 1.35 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1217 1.31 - 1.43: 2275 1.43 - 1.56: 4932 1.56 - 1.68: 16 1.68 - 1.81: 66 Bond restraints: 8506 Sorted by residual: bond pdb=" CA TYR B 486 " pdb=" C TYR B 486 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" C1A PIO A1003 " pdb=" O2C PIO A1003 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1A PIO B1001 " pdb=" O2C PIO B1001 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C CO3 B1004 " pdb=" O1 CO3 B1004 " ideal model delta sigma weight residual 1.285 1.217 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1B PIO A1003 " pdb=" O3C PIO A1003 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 8501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11381 2.53 - 5.07: 135 5.07 - 7.60: 22 7.60 - 10.14: 6 10.14 - 12.67: 4 Bond angle restraints: 11548 Sorted by residual: angle pdb=" O1 PIO B1001 " pdb=" P1 PIO B1001 " pdb=" O13 PIO B1001 " ideal model delta sigma weight residual 97.64 110.31 -12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O1 PIO A1003 " pdb=" P1 PIO A1003 " pdb=" O13 PIO A1003 " ideal model delta sigma weight residual 97.64 109.67 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 PIO B1001 " pdb=" P1 PIO B1001 " pdb=" O12 PIO B1001 " ideal model delta sigma weight residual 121.09 109.45 11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 PIO A1003 " pdb=" P1 PIO A1003 " pdb=" O12 PIO A1003 " ideal model delta sigma weight residual 121.09 109.66 11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C2A PIO B1001 " pdb=" C1A PIO B1001 " pdb=" O2C PIO B1001 " ideal model delta sigma weight residual 110.66 120.65 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 11543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.12: 4617 25.12 - 50.24: 378 50.24 - 75.36: 36 75.36 - 100.48: 3 100.48 - 125.61: 6 Dihedral angle restraints: 5040 sinusoidal: 2094 harmonic: 2946 Sorted by residual: dihedral pdb=" C3 PLC B1003 " pdb=" C1 PLC B1003 " pdb=" C2 PLC B1003 " pdb=" O3P PLC B1003 " ideal model delta sinusoidal sigma weight residual 67.16 -167.23 -125.61 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" O2 PLC B1003 " pdb=" C1 PLC B1003 " pdb=" C2 PLC B1003 " pdb=" O3P PLC B1003 " ideal model delta sinusoidal sigma weight residual -55.71 69.56 -125.27 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" O2 PLC A1001 " pdb=" C1 PLC A1001 " pdb=" C2 PLC A1001 " pdb=" O3P PLC A1001 " ideal model delta sinusoidal sigma weight residual -55.71 -177.88 122.17 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 942 0.033 - 0.066: 288 0.066 - 0.099: 103 0.099 - 0.133: 31 0.133 - 0.166: 4 Chirality restraints: 1368 Sorted by residual: chirality pdb=" C2C PIO A1003 " pdb=" C1C PIO A1003 " pdb=" C3C PIO A1003 " pdb=" O2C PIO A1003 " both_signs ideal model delta sigma weight residual False -2.56 -2.39 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR B 798 " pdb=" CA THR B 798 " pdb=" OG1 THR B 798 " pdb=" CG2 THR B 798 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ARG B 730 " pdb=" N ARG B 730 " pdb=" C ARG B 730 " pdb=" CB ARG B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 1365 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CO3 B1004 " -0.091 2.00e-02 2.50e+03 5.25e-02 2.75e+01 pdb=" O1 CO3 B1004 " 0.030 2.00e-02 2.50e+03 pdb=" O2 CO3 B1004 " 0.030 2.00e-02 2.50e+03 pdb=" O3 CO3 B1004 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 390 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 391 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 390 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO B 391 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 391 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 391 " 0.033 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1970 2.79 - 3.32: 8173 3.32 - 3.84: 14027 3.84 - 4.37: 15712 4.37 - 4.90: 28318 Nonbonded interactions: 68200 Sorted by model distance: nonbonded pdb=" OH TYR B 393 " pdb=" O LEU B 453 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLU A 472 " pdb=" OH TYR A 486 " model vdw 2.263 3.040 nonbonded pdb=" NH2 ARG B 518 " pdb=" OE2 GLU B 693 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR A 520 " pdb=" OG1 THR A 866 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG A 808 " pdb=" OE1 GLN A 840 " model vdw 2.340 3.120 ... (remaining 68195 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 370 through 889 or resid 1002 or resid 1004 through 1005)) \ selection = (chain 'B' and (resid 370 through 889 or (resid 1002 and (name CB or name OB or \ name C' or name C1 or name C1' or name C1B or name C2 or name C2' or name C2B or \ name C3 or name C3' or name C3B or name C4' or name C4B or name C5' or name C5B \ or name C6' or name C6B or name C7' or name C7B or name C8' or name O' or name \ O1P or name O2 or name O2P or name O3 or name O3P or name O4P or name P )) or re \ sid 1004 through 1005)) } 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: 2.560 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.070 8508 Z= 0.199 Angle : 0.691 12.669 11554 Z= 0.314 Chirality : 0.039 0.166 1368 Planarity : 0.005 0.061 1390 Dihedral : 17.216 125.606 3140 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.45 % Allowed : 23.65 % Favored : 75.90 % 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: 1.97 (0.27), residues: 1014 helix: 1.98 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.023 0.002 TYR B 486 PHE 0.018 0.001 PHE A 476 TRP 0.016 0.001 TRP A 662 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 ( 8506) covalent geometry : angle 0.68985 / 0.31 (11548) hydrogen bonds : bond 0.12179 / 8.27 ( 548) hydrogen bonds : angle 4.91820 / 3.62 ( 1581) link_NAG-ASN : bond 0.00085 / 0.04 ( 2) link_NAG-ASN : angle 1.53591 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.297 Fit side-chains REVERT: B 430 LYS cc_start: 0.7503 (mmmt) cc_final: 0.7292 (mmmt) outliers start: 4 outliers final: 2 residues processed: 119 average time/residue: 0.0718 time to fit residues: 13.0154 Evaluate side-chains 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 640 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 759 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127874 restraints weight = 11265.851| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.98 r_work: 0.3389 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8508 Z= 0.184 Angle : 0.578 6.358 11554 Z= 0.286 Chirality : 0.042 0.131 1368 Planarity : 0.005 0.061 1390 Dihedral : 10.056 87.858 1265 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.38 % Allowed : 20.72 % Favored : 75.90 % 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: 1.78 (0.27), residues: 1014 helix: 1.88 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 514 TYR 0.019 0.002 TYR A 555 PHE 0.016 0.002 PHE B 478 TRP 0.011 0.002 TRP A 492 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 8506) covalent geometry : angle 0.57694 / 0.29 (11548) hydrogen bonds : bond 0.04711 / 3.18 ( 548) hydrogen bonds : angle 4.34350 / 3.19 ( 1581) link_NAG-ASN : bond 0.00124 / 0.06 ( 2) link_NAG-ASN : angle 1.81465 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.305 Fit side-chains REVERT: B 382 LEU cc_start: 0.8160 (tp) cc_final: 0.7814 (tp) REVERT: B 476 PHE cc_start: 0.8041 (t80) cc_final: 0.7699 (t80) REVERT: B 658 GLU cc_start: 0.6670 (tp30) cc_final: 0.6380 (mm-30) REVERT: A 661 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6098 (mm) REVERT: A 721 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6150 (mtp) REVERT: A 865 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7503 (mp) outliers start: 30 outliers final: 13 residues processed: 143 average time/residue: 0.0689 time to fit residues: 15.2373 Evaluate side-chains 126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 865 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.0000 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN B 759 GLN A 482 ASN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132609 restraints weight = 11129.732| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.96 r_work: 0.3448 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8508 Z= 0.111 Angle : 0.508 6.372 11554 Z= 0.251 Chirality : 0.039 0.139 1368 Planarity : 0.005 0.059 1390 Dihedral : 8.869 82.747 1262 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.82 % Allowed : 20.95 % Favored : 76.24 % 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: 2.08 (0.27), residues: 1014 helix: 2.16 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.018 0.001 TYR A 413 PHE 0.014 0.001 PHE B 478 TRP 0.009 0.001 TRP B 496 HIS 0.002 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8506) covalent geometry : angle 0.50654 / 0.25 (11548) hydrogen bonds : bond 0.03964 / 2.66 ( 548) hydrogen bonds : angle 4.11384 / 3.03 ( 1581) link_NAG-ASN : bond 0.00141 / 0.07 ( 2) link_NAG-ASN : angle 1.64945 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.312 Fit side-chains REVERT: B 382 LEU cc_start: 0.8176 (tp) cc_final: 0.7798 (tp) REVERT: B 401 PHE cc_start: 0.6213 (t80) cc_final: 0.5892 (t80) REVERT: B 476 PHE cc_start: 0.8028 (t80) cc_final: 0.7627 (t80) REVERT: B 543 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8273 (tt) REVERT: B 658 GLU cc_start: 0.6581 (tp30) cc_final: 0.6290 (mm-30) REVERT: A 401 PHE cc_start: 0.6047 (t80) cc_final: 0.5780 (t80) REVERT: A 672 LEU cc_start: 0.8471 (tp) cc_final: 0.8252 (tt) REVERT: A 774 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7464 (mp) outliers start: 25 outliers final: 8 residues processed: 141 average time/residue: 0.0661 time to fit residues: 14.4811 Evaluate side-chains 124 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN B 759 GLN A 482 ASN A 651 HIS A 759 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132315 restraints weight = 11373.607| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.99 r_work: 0.3444 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8508 Z= 0.114 Angle : 0.506 7.608 11554 Z= 0.247 Chirality : 0.039 0.132 1368 Planarity : 0.005 0.057 1390 Dihedral : 8.217 80.882 1262 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.72 % Allowed : 20.38 % Favored : 75.90 % 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: 2.35 (0.27), residues: 1014 helix: 2.30 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.017 0.001 TYR A 555 PHE 0.015 0.001 PHE B 478 TRP 0.009 0.001 TRP B 496 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8506) covalent geometry : angle 0.50456 / 0.25 (11548) hydrogen bonds : bond 0.03899 / 2.62 ( 548) hydrogen bonds : angle 4.05953 / 2.98 ( 1581) link_NAG-ASN : bond 0.00077 / 0.04 ( 2) link_NAG-ASN : angle 1.65275 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.275 Fit side-chains REVERT: B 382 LEU cc_start: 0.8200 (tp) cc_final: 0.7825 (tp) REVERT: B 401 PHE cc_start: 0.6086 (t80) cc_final: 0.5738 (t80) REVERT: B 476 PHE cc_start: 0.8034 (t80) cc_final: 0.7628 (t80) REVERT: B 543 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 658 GLU cc_start: 0.6574 (tp30) cc_final: 0.6324 (mm-30) REVERT: A 401 PHE cc_start: 0.6083 (t80) cc_final: 0.5844 (t80) REVERT: A 721 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.5902 (mtp) REVERT: A 724 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 774 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7418 (mp) outliers start: 33 outliers final: 17 residues processed: 147 average time/residue: 0.0521 time to fit residues: 11.8254 Evaluate side-chains 129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 865 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.0570 chunk 90 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132804 restraints weight = 11261.123| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.98 r_work: 0.3454 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8508 Z= 0.114 Angle : 0.510 7.903 11554 Z= 0.248 Chirality : 0.039 0.134 1368 Planarity : 0.005 0.056 1390 Dihedral : 7.907 80.404 1262 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.49 % Allowed : 20.50 % Favored : 76.01 % 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: 2.17 (0.27), residues: 1014 helix: 2.16 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 514 TYR 0.016 0.001 TYR A 555 PHE 0.017 0.001 PHE A 478 TRP 0.009 0.001 TRP B 496 HIS 0.002 0.000 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8506) covalent geometry : angle 0.50922 / 0.25 (11548) hydrogen bonds : bond 0.03847 / 2.58 ( 548) hydrogen bonds : angle 4.00492 / 2.95 ( 1581) link_NAG-ASN : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : angle 1.65876 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.302 Fit side-chains REVERT: B 401 PHE cc_start: 0.6060 (t80) cc_final: 0.5747 (t80) REVERT: B 476 PHE cc_start: 0.8051 (t80) cc_final: 0.7628 (t80) REVERT: B 543 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 658 GLU cc_start: 0.6607 (tp30) cc_final: 0.6357 (mm-30) REVERT: A 507 PHE cc_start: 0.7419 (m-10) cc_final: 0.7208 (m-10) REVERT: A 721 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.5866 (mtp) REVERT: A 724 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 774 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7477 (mp) outliers start: 31 outliers final: 19 residues processed: 137 average time/residue: 0.0581 time to fit residues: 12.6007 Evaluate side-chains 129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 759 GLN A 651 HIS A 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130679 restraints weight = 11207.854| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.95 r_work: 0.3440 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8508 Z= 0.124 Angle : 0.510 5.964 11554 Z= 0.250 Chirality : 0.039 0.133 1368 Planarity : 0.005 0.055 1390 Dihedral : 7.847 79.574 1262 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.83 % Allowed : 20.38 % Favored : 75.79 % 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: 2.11 (0.27), residues: 1014 helix: 2.11 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.016 0.001 TYR A 555 PHE 0.017 0.001 PHE A 478 TRP 0.008 0.001 TRP B 496 HIS 0.002 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8506) covalent geometry : angle 0.50847 / 0.25 (11548) hydrogen bonds : bond 0.03933 / 2.65 ( 548) hydrogen bonds : angle 4.03527 / 2.96 ( 1581) link_NAG-ASN : bond 0.00043 / 0.02 ( 2) link_NAG-ASN : angle 1.74397 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.268 Fit side-chains REVERT: B 401 PHE cc_start: 0.6055 (t80) cc_final: 0.5769 (t80) REVERT: B 476 PHE cc_start: 0.8080 (t80) cc_final: 0.7640 (t80) REVERT: B 543 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8300 (tt) REVERT: B 658 GLU cc_start: 0.6679 (tp30) cc_final: 0.6425 (mm-30) REVERT: B 776 MET cc_start: 0.8664 (mtp) cc_final: 0.8393 (mtp) REVERT: A 721 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.5965 (mtp) REVERT: A 724 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 774 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7497 (mp) outliers start: 34 outliers final: 20 residues processed: 144 average time/residue: 0.0633 time to fit residues: 14.3628 Evaluate side-chains 129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132477 restraints weight = 11250.511| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.96 r_work: 0.3450 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8508 Z= 0.117 Angle : 0.515 8.582 11554 Z= 0.250 Chirality : 0.039 0.133 1368 Planarity : 0.005 0.055 1390 Dihedral : 7.713 80.037 1262 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.94 % Allowed : 20.27 % Favored : 75.79 % 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: 2.15 (0.27), residues: 1014 helix: 2.14 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.015 0.001 TYR A 555 PHE 0.019 0.001 PHE A 478 TRP 0.009 0.001 TRP B 496 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8506) covalent geometry : angle 0.51327 / 0.25 (11548) hydrogen bonds : bond 0.03857 / 2.59 ( 548) hydrogen bonds : angle 4.00191 / 2.95 ( 1581) link_NAG-ASN : bond 0.00072 / 0.03 ( 2) link_NAG-ASN : angle 1.70388 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.312 Fit side-chains REVERT: B 401 PHE cc_start: 0.6114 (t80) cc_final: 0.5777 (t80) REVERT: B 476 PHE cc_start: 0.8080 (t80) cc_final: 0.7607 (t80) REVERT: B 543 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 658 GLU cc_start: 0.6746 (tp30) cc_final: 0.6497 (mm-30) REVERT: B 776 MET cc_start: 0.8621 (mtp) cc_final: 0.8328 (mtp) REVERT: A 507 PHE cc_start: 0.7407 (m-10) cc_final: 0.7198 (m-10) REVERT: A 721 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5906 (mtp) REVERT: A 724 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8496 (mt) REVERT: A 774 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7489 (mp) outliers start: 35 outliers final: 20 residues processed: 134 average time/residue: 0.0627 time to fit residues: 13.3205 Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131894 restraints weight = 11164.609| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.95 r_work: 0.3442 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8508 Z= 0.123 Angle : 0.511 7.531 11554 Z= 0.250 Chirality : 0.039 0.134 1368 Planarity : 0.005 0.055 1390 Dihedral : 7.598 79.416 1262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.49 % Allowed : 20.61 % Favored : 75.90 % 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: 2.11 (0.27), residues: 1014 helix: 2.10 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.015 0.001 TYR A 555 PHE 0.019 0.001 PHE A 478 TRP 0.008 0.001 TRP A 492 HIS 0.002 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8506) covalent geometry : angle 0.50956 / 0.25 (11548) hydrogen bonds : bond 0.03911 / 2.63 ( 548) hydrogen bonds : angle 4.02672 / 2.96 ( 1581) link_NAG-ASN : bond 0.00043 / 0.02 ( 2) link_NAG-ASN : angle 1.74077 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.300 Fit side-chains REVERT: B 401 PHE cc_start: 0.6126 (t80) cc_final: 0.5688 (t80) REVERT: B 476 PHE cc_start: 0.8107 (t80) cc_final: 0.7636 (t80) REVERT: B 543 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8302 (tt) REVERT: B 658 GLU cc_start: 0.6609 (tp30) cc_final: 0.6346 (mm-30) REVERT: B 776 MET cc_start: 0.8657 (mtp) cc_final: 0.8361 (mtp) REVERT: A 507 PHE cc_start: 0.7367 (m-10) cc_final: 0.7150 (m-10) REVERT: A 721 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.5983 (mtp) REVERT: A 724 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 774 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7478 (mp) outliers start: 31 outliers final: 23 residues processed: 138 average time/residue: 0.0615 time to fit residues: 13.4190 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130635 restraints weight = 11241.398| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.96 r_work: 0.3426 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8508 Z= 0.138 Angle : 0.532 7.695 11554 Z= 0.261 Chirality : 0.040 0.141 1368 Planarity : 0.005 0.055 1390 Dihedral : 7.569 78.343 1262 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.83 % Allowed : 20.50 % Favored : 75.68 % 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: 2.03 (0.27), residues: 1014 helix: 2.05 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.015 0.002 TYR A 555 PHE 0.018 0.001 PHE A 478 TRP 0.009 0.001 TRP B 848 HIS 0.002 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8506) covalent geometry : angle 0.53047 / 0.26 (11548) hydrogen bonds : bond 0.04097 / 2.76 ( 548) hydrogen bonds : angle 4.08090 / 2.99 ( 1581) link_NAG-ASN : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : angle 1.85483 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.308 Fit side-chains REVERT: B 401 PHE cc_start: 0.6137 (t80) cc_final: 0.5823 (t80) REVERT: B 476 PHE cc_start: 0.8131 (t80) cc_final: 0.7616 (t80) REVERT: B 543 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 658 GLU cc_start: 0.6619 (tp30) cc_final: 0.6352 (mm-30) REVERT: B 776 MET cc_start: 0.8672 (mtp) cc_final: 0.8397 (mtp) REVERT: A 507 PHE cc_start: 0.7485 (m-10) cc_final: 0.7268 (m-10) REVERT: A 721 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6077 (mtp) REVERT: A 774 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7483 (mp) outliers start: 34 outliers final: 26 residues processed: 139 average time/residue: 0.0578 time to fit residues: 12.6138 Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130986 restraints weight = 11278.199| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.97 r_work: 0.3430 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8508 Z= 0.132 Angle : 0.525 7.586 11554 Z= 0.258 Chirality : 0.040 0.140 1368 Planarity : 0.005 0.056 1390 Dihedral : 7.496 78.590 1262 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.38 % Allowed : 20.72 % Favored : 75.90 % 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: 2.00 (0.27), residues: 1014 helix: 2.07 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.017 0.002 TYR A 413 PHE 0.019 0.001 PHE A 478 TRP 0.009 0.001 TRP A 492 HIS 0.003 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8506) covalent geometry : angle 0.52316 / 0.26 (11548) hydrogen bonds : bond 0.04033 / 2.71 ( 548) hydrogen bonds : angle 4.08687 / 3.00 ( 1581) link_NAG-ASN : bond 0.00030 / 0.01 ( 2) link_NAG-ASN : angle 1.85356 / 1.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.320 Fit side-chains REVERT: B 401 PHE cc_start: 0.6116 (t80) cc_final: 0.5695 (t80) REVERT: B 476 PHE cc_start: 0.8126 (t80) cc_final: 0.7634 (t80) REVERT: B 658 GLU cc_start: 0.6630 (tp30) cc_final: 0.6359 (mm-30) REVERT: B 776 MET cc_start: 0.8683 (mtp) cc_final: 0.8414 (mtp) REVERT: A 507 PHE cc_start: 0.7447 (m-10) cc_final: 0.7233 (m-10) REVERT: A 721 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6023 (mtp) REVERT: A 774 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7488 (mp) outliers start: 30 outliers final: 28 residues processed: 129 average time/residue: 0.0602 time to fit residues: 12.1363 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 774 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131477 restraints weight = 11233.151| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.96 r_work: 0.3438 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.127 Angle : 0.522 7.256 11554 Z= 0.257 Chirality : 0.040 0.142 1368 Planarity : 0.005 0.056 1390 Dihedral : 7.353 78.518 1262 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.38 % Allowed : 21.06 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1014 helix: 2.08 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.015 0.001 TYR B 824 PHE 0.019 0.001 PHE A 478 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8506) covalent geometry : angle 0.52066 / 0.26 (11548) hydrogen bonds : bond 0.03985 / 2.68 ( 548) hydrogen bonds : angle 4.07322 / 2.99 ( 1581) link_NAG-ASN : bond 0.00030 / 0.01 ( 2) link_NAG-ASN : angle 1.84789 / 1.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.98 seconds wall clock time: 34 minutes 19.77 seconds (2059.77 seconds total)