Starting phenix.real_space_refine on Sat Jul 4 02:47:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422.map" model { file = "/net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mng_48422/07_2026/9mng_48422_trim.cif" } resolution = 3.11 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= 0.003 sd= 0.044 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 36 5.16 5 C 5574 2.51 5 N 1305 2.21 5 O 1425 1.98 5 H 8502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16850 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8310 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8310 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.01, per 1000 atoms: 0.18 Number of scatterers: 16850 At special positions: 0 Unit cell: (83.6785, 70.4225, 135.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 8 15.00 O 1425 8.00 N 1305 7.00 C 5574 6.00 H 8502 1.00 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 BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG B1001 " - " ASN B 642 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 505.7 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 76.5% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 402 through 431 removed outlier: 3.518A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 483 Processing helix chain 'C' and resid 485 through 507 Processing helix chain 'C' and resid 508 through 516 Processing helix chain 'C' and resid 517 through 547 Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.883A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 608 through 624 Processing helix chain 'C' and resid 660 through 667 Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 701 through 720 removed outlier: 3.557A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 760 through 773 Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 800 removed outlier: 3.776A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 removed outlier: 3.976A pdb=" N PHE C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 822 through 828 Processing helix chain 'C' and resid 829 through 853 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 858 through 872 removed outlier: 3.984A pdb=" N VAL C 867 " --> pdb=" O LEU C 863 " (cutoff:3.500A) Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 872 through 878 removed outlier: 4.136A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 400 removed outlier: 3.578A pdb=" N ILE B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 432 removed outlier: 3.526A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) 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 508 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 594 removed outlier: 3.726A 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 624 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 720 removed outlier: 3.626A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 800 removed outlier: 3.811A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 814 removed outlier: 3.909A pdb=" N PHE B 813 " --> pdb=" O ILE B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 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 Processing helix chain 'B' and resid 872 through 878 removed outlier: 4.002A pdb=" N LEU B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'C' and resid 739 through 742 removed outlier: 5.741A pdb=" N GLY C 742 " --> pdb=" O ILE C 753 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 753 " --> pdb=" O GLY C 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 5.928A pdb=" N GLY B 742 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE B 753 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1617 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: 3.92 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8496 1.03 - 1.23: 22 1.23 - 1.42: 3432 1.42 - 1.62: 5026 1.62 - 1.81: 78 Bond restraints: 17054 Sorted by residual: bond pdb=" C1A PIO B1002 " pdb=" O2C PIO B1002 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1B PIO C1001 " pdb=" O3C PIO C1001 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1B PIO B1002 " pdb=" O3C PIO B1002 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O4 PIO B1002 " pdb=" P4 PIO B1002 " ideal model delta sigma weight residual 1.710 1.647 0.063 2.00e-02 2.50e+03 9.85e+00 ... (remaining 17049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 30735 2.40 - 4.80: 140 4.80 - 7.20: 22 7.20 - 9.61: 6 9.61 - 12.01: 4 Bond angle restraints: 30907 Sorted by residual: angle pdb=" O1 PIO C1001 " pdb=" P1 PIO C1001 " pdb=" O13 PIO C1001 " ideal model delta sigma weight residual 97.64 109.65 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 PIO C1001 " pdb=" P1 PIO C1001 " pdb=" O12 PIO C1001 " ideal model delta sigma weight residual 121.09 109.36 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PIO B1002 " pdb=" P1 PIO B1002 " pdb=" O12 PIO B1002 " ideal model delta sigma weight residual 121.09 109.65 11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O1 PIO B1002 " pdb=" P1 PIO B1002 " pdb=" O13 PIO B1002 " ideal model delta sigma weight residual 97.64 108.72 -11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C2A PIO C1001 " pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 110.66 119.67 -9.01 3.00e+00 1.11e-01 9.02e+00 ... (remaining 30902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6966 17.70 - 35.39: 738 35.39 - 53.09: 257 53.09 - 70.79: 93 70.79 - 88.49: 16 Dihedral angle restraints: 8070 sinusoidal: 4436 harmonic: 3634 Sorted by residual: dihedral pdb=" CA ASP B 821 " pdb=" CB ASP B 821 " pdb=" CG ASP B 821 " pdb=" OD1 ASP B 821 " ideal model delta sinusoidal sigma weight residual -30.00 -86.37 56.37 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 658 " pdb=" CG GLU B 658 " pdb=" CD GLU B 658 " pdb=" OE1 GLU B 658 " ideal model delta sinusoidal sigma weight residual 0.00 -88.49 88.49 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 480 " pdb=" CG GLU B 480 " pdb=" CD GLU B 480 " pdb=" OE1 GLU B 480 " ideal model delta sinusoidal sigma weight residual 0.00 86.98 -86.98 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 860 0.026 - 0.051: 303 0.051 - 0.077: 140 0.077 - 0.103: 59 0.103 - 0.128: 26 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA VAL B 634 " pdb=" N VAL B 634 " pdb=" C VAL B 634 " pdb=" CB VAL B 634 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 624 " pdb=" N ILE B 624 " pdb=" C ILE B 624 " pdb=" CB ILE B 624 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE C 624 " pdb=" N ILE C 624 " pdb=" C ILE C 624 " pdb=" CB ILE C 624 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 1385 not shown) Planarity restraints: 2371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 867 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 868 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 868 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 868 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 610 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 611 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 874 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO B 875 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 875 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 875 " -0.023 5.00e-02 4.00e+02 ... (remaining 2368 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 8540 2.43 - 2.97: 39912 2.97 - 3.52: 47857 3.52 - 4.06: 60181 4.06 - 4.60: 90221 Nonbonded interactions: 246711 Sorted by model distance: nonbonded pdb=" H SER B 438 " pdb=" HG SER B 438 " model vdw 1.890 2.100 nonbonded pdb=" HE2 PHE C 471 " pdb=" HZ2 TRP C 723 " model vdw 1.892 2.100 nonbonded pdb=" H SER B 856 " pdb=" HG SER B 856 " model vdw 1.898 2.100 nonbonded pdb="HE22 GLN C 759 " pdb=" HG SER C 762 " model vdw 1.905 2.100 nonbonded pdb=" H SER C 856 " pdb=" HG SER C 856 " model vdw 1.907 2.100 ... (remaining 246706 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 'B' and resid 371 through 894) selection = (chain 'C' and resid 371 through 894) } 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=0.00 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: 4.800 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.790 Find NCS groups from input model: 0.250 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8556 Z= 0.161 Angle : 0.653 12.007 11633 Z= 0.284 Chirality : 0.037 0.128 1388 Planarity : 0.004 0.047 1395 Dihedral : 17.797 88.487 3164 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.06 (0.26), residues: 1026 helix: 1.88 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.24 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.009 0.001 TYR C 486 PHE 0.014 0.001 PHE B 471 TRP 0.012 0.001 TRP C 492 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 8552) covalent geometry : angle 0.65212 / 0.28 (11621) hydrogen bonds : bond 0.12606 / 8.53 ( 560) hydrogen bonds : angle 5.36398 / 3.96 ( 1617) link_BETA1-4 : bond 0.00522 / 0.35 ( 1) link_BETA1-4 : angle 1.11901 / 0.93 ( 3) link_BETA1-6 : bond 0.00466 / 0.31 ( 1) link_BETA1-6 : angle 1.46738 / 1.24 ( 3) link_NAG-ASN : bond 0.00101 / 0.07 ( 2) link_NAG-ASN : angle 1.11167 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 MET cc_start: 0.8157 (mmp) cc_final: 0.7866 (mmp) REVERT: B 392 TYR cc_start: 0.7664 (m-80) cc_final: 0.7293 (m-80) outliers start: 16 outliers final: 15 residues processed: 66 average time/residue: 0.1422 time to fit residues: 15.4292 Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 833 MET Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.109209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089220 restraints weight = 49610.224| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.13 r_work: 0.3342 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8556 Z= 0.168 Angle : 0.526 4.934 11633 Z= 0.267 Chirality : 0.038 0.135 1388 Planarity : 0.005 0.046 1395 Dihedral : 10.999 85.478 1319 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 18.62 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.05 (0.26), residues: 1026 helix: 1.89 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.21 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 602 TYR 0.011 0.001 TYR C 824 PHE 0.013 0.001 PHE B 471 TRP 0.010 0.001 TRP C 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 8552) covalent geometry : angle 0.52454 / 0.27 (11621) hydrogen bonds : bond 0.04955 / 3.34 ( 560) hydrogen bonds : angle 4.60685 / 3.39 ( 1617) link_BETA1-4 : bond 0.00095 / 0.06 ( 1) link_BETA1-4 : angle 1.00364 / 0.75 ( 3) link_BETA1-6 : bond 0.00297 / 0.20 ( 1) link_BETA1-6 : angle 1.51564 / 1.26 ( 3) link_NAG-ASN : bond 0.00146 / 0.10 ( 2) link_NAG-ASN : angle 1.16720 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 587 MET cc_start: 0.8265 (mmp) cc_final: 0.8043 (mmp) REVERT: C 729 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7984 (t) REVERT: B 392 TYR cc_start: 0.7596 (m-80) cc_final: 0.7221 (m-80) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.1414 time to fit residues: 14.8253 Evaluate side-chains 61 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 677 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086739 restraints weight = 50496.009| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.14 r_work: 0.3292 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8556 Z= 0.247 Angle : 0.579 6.028 11633 Z= 0.298 Chirality : 0.041 0.181 1388 Planarity : 0.005 0.046 1395 Dihedral : 11.123 82.728 1302 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.16 % Allowed : 17.49 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.72 (0.25), residues: 1026 helix: 1.69 (0.19), residues: 688 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 602 TYR 0.013 0.002 TYR B 486 PHE 0.013 0.002 PHE C 836 TRP 0.013 0.002 TRP C 492 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 ( 8552) covalent geometry : angle 0.57767 / 0.30 (11621) hydrogen bonds : bond 0.05181 / 3.49 ( 560) hydrogen bonds : angle 4.68894 / 3.44 ( 1617) link_BETA1-4 : bond 0.00208 / 0.14 ( 1) link_BETA1-4 : angle 0.97530 / 0.71 ( 3) link_BETA1-6 : bond 0.00197 / 0.13 ( 1) link_BETA1-6 : angle 1.77529 / 1.42 ( 3) link_NAG-ASN : bond 0.00184 / 0.13 ( 2) link_NAG-ASN : angle 1.53976 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8044 (t) REVERT: C 759 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7181 (pp30) REVERT: B 723 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.7686 (p90) outliers start: 28 outliers final: 21 residues processed: 75 average time/residue: 0.1510 time to fit residues: 17.7994 Evaluate side-chains 75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 648 TRP Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 890 ASP Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 723 TRP Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.108639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088712 restraints weight = 49303.200| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.11 r_work: 0.3330 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8556 Z= 0.128 Angle : 0.504 5.250 11633 Z= 0.255 Chirality : 0.038 0.173 1388 Planarity : 0.004 0.045 1395 Dihedral : 10.605 82.515 1300 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 18.85 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.25), residues: 1026 helix: 2.00 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 602 TYR 0.013 0.001 TYR B 486 PHE 0.014 0.001 PHE B 471 TRP 0.012 0.001 TRP C 492 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8552) covalent geometry : angle 0.50321 / 0.26 (11621) hydrogen bonds : bond 0.04487 / 3.04 ( 560) hydrogen bonds : angle 4.43824 / 3.26 ( 1617) link_BETA1-4 : bond 0.00473 / 0.32 ( 1) link_BETA1-4 : angle 1.08593 / 0.79 ( 3) link_BETA1-6 : bond 0.00541 / 0.36 ( 1) link_BETA1-6 : angle 1.49851 / 1.21 ( 3) link_NAG-ASN : bond 0.00163 / 0.11 ( 2) link_NAG-ASN : angle 1.10453 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7977 (t) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1396 time to fit residues: 14.4649 Evaluate side-chains 59 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 648 TRP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.108724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088786 restraints weight = 49228.890| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.11 r_work: 0.3333 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8556 Z= 0.136 Angle : 0.499 5.308 11633 Z= 0.252 Chirality : 0.038 0.158 1388 Planarity : 0.004 0.044 1395 Dihedral : 10.235 82.627 1299 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 18.17 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.13 (0.25), residues: 1026 helix: 2.08 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 490 TYR 0.014 0.001 TYR B 486 PHE 0.013 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8552) covalent geometry : angle 0.49810 / 0.25 (11621) hydrogen bonds : bond 0.04358 / 2.95 ( 560) hydrogen bonds : angle 4.35953 / 3.21 ( 1617) link_BETA1-4 : bond 0.00266 / 0.18 ( 1) link_BETA1-4 : angle 1.05533 / 0.77 ( 3) link_BETA1-6 : bond 0.00296 / 0.20 ( 1) link_BETA1-6 : angle 1.42274 / 1.15 ( 3) link_NAG-ASN : bond 0.00160 / 0.11 ( 2) link_NAG-ASN : angle 1.10378 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7975 (t) REVERT: B 853 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (t) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.1487 time to fit residues: 15.7219 Evaluate side-chains 62 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088145 restraints weight = 49445.762| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.13 r_work: 0.3320 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8556 Z= 0.171 Angle : 0.516 5.528 11633 Z= 0.262 Chirality : 0.039 0.162 1388 Planarity : 0.005 0.044 1395 Dihedral : 10.100 83.365 1296 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.82 % Allowed : 17.49 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.25), residues: 1026 helix: 2.01 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 602 TYR 0.014 0.001 TYR B 486 PHE 0.013 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 8552) covalent geometry : angle 0.51481 / 0.26 (11621) hydrogen bonds : bond 0.04486 / 3.03 ( 560) hydrogen bonds : angle 4.39087 / 3.23 ( 1617) link_BETA1-4 : bond 0.00340 / 0.23 ( 1) link_BETA1-4 : angle 1.09373 / 0.78 ( 3) link_BETA1-6 : bond 0.00228 / 0.15 ( 1) link_BETA1-6 : angle 1.44674 / 1.15 ( 3) link_NAG-ASN : bond 0.00182 / 0.12 ( 2) link_NAG-ASN : angle 1.18223 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7972 (t) REVERT: C 759 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7111 (pp30) REVERT: B 853 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8366 (t) outliers start: 25 outliers final: 17 residues processed: 69 average time/residue: 0.1339 time to fit residues: 15.0254 Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 833 MET Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.108670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088739 restraints weight = 49380.699| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.12 r_work: 0.3329 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8556 Z= 0.137 Angle : 0.499 5.327 11633 Z= 0.252 Chirality : 0.038 0.163 1388 Planarity : 0.004 0.044 1395 Dihedral : 9.944 83.469 1296 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.14 % Allowed : 18.28 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.12 (0.25), residues: 1026 helix: 2.08 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.10 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 602 TYR 0.012 0.001 TYR B 486 PHE 0.013 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8552) covalent geometry : angle 0.49803 / 0.25 (11621) hydrogen bonds : bond 0.04320 / 2.92 ( 560) hydrogen bonds : angle 4.32625 / 3.18 ( 1617) link_BETA1-4 : bond 0.00298 / 0.20 ( 1) link_BETA1-4 : angle 1.08865 / 0.79 ( 3) link_BETA1-6 : bond 0.00354 / 0.24 ( 1) link_BETA1-6 : angle 1.42617 / 1.13 ( 3) link_NAG-ASN : bond 0.00162 / 0.11 ( 2) link_NAG-ASN : angle 1.12059 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7971 (t) REVERT: C 759 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7089 (pp30) REVERT: B 853 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (t) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1415 time to fit residues: 15.3856 Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087679 restraints weight = 49859.681| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.12 r_work: 0.3311 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8556 Z= 0.192 Angle : 0.528 5.690 11633 Z= 0.268 Chirality : 0.039 0.163 1388 Planarity : 0.005 0.045 1395 Dihedral : 10.103 84.177 1296 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.71 % Allowed : 17.61 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.95 (0.25), residues: 1026 helix: 1.95 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.01 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 602 TYR 0.013 0.002 TYR B 486 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 8552) covalent geometry : angle 0.52682 / 0.27 (11621) hydrogen bonds : bond 0.04553 / 3.07 ( 560) hydrogen bonds : angle 4.40360 / 3.23 ( 1617) link_BETA1-4 : bond 0.00270 / 0.18 ( 1) link_BETA1-4 : angle 1.07030 / 0.77 ( 3) link_BETA1-6 : bond 0.00317 / 0.21 ( 1) link_BETA1-6 : angle 1.51463 / 1.20 ( 3) link_NAG-ASN : bond 0.00169 / 0.11 ( 2) link_NAG-ASN : angle 1.25299 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7991 (t) REVERT: C 759 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7070 (pp30) REVERT: B 853 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (t) outliers start: 24 outliers final: 19 residues processed: 69 average time/residue: 0.1472 time to fit residues: 16.3326 Evaluate side-chains 68 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 648 TRP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 833 MET Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088980 restraints weight = 49326.491| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.12 r_work: 0.3336 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8556 Z= 0.122 Angle : 0.492 5.232 11633 Z= 0.248 Chirality : 0.038 0.168 1388 Planarity : 0.004 0.044 1395 Dihedral : 9.786 84.208 1296 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.37 % Allowed : 17.95 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.18 (0.26), residues: 1026 helix: 2.14 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.09 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 602 TYR 0.011 0.001 TYR B 486 PHE 0.014 0.001 PHE B 471 TRP 0.012 0.001 TRP C 492 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8552) covalent geometry : angle 0.49034 / 0.25 (11621) hydrogen bonds : bond 0.04194 / 2.84 ( 560) hydrogen bonds : angle 4.27138 / 3.14 ( 1617) link_BETA1-4 : bond 0.00373 / 0.25 ( 1) link_BETA1-4 : angle 1.16116 / 0.86 ( 3) link_BETA1-6 : bond 0.00367 / 0.24 ( 1) link_BETA1-6 : angle 1.32516 / 1.06 ( 3) link_NAG-ASN : bond 0.00179 / 0.12 ( 2) link_NAG-ASN : angle 1.09683 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7934 (t) REVERT: C 759 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: B 392 TYR cc_start: 0.7676 (m-80) cc_final: 0.7320 (m-80) REVERT: B 853 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8360 (t) outliers start: 21 outliers final: 17 residues processed: 67 average time/residue: 0.1413 time to fit residues: 15.4715 Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 648 TRP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.108608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088840 restraints weight = 49219.897| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.12 r_work: 0.3332 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8556 Z= 0.135 Angle : 0.494 5.262 11633 Z= 0.249 Chirality : 0.038 0.159 1388 Planarity : 0.004 0.044 1395 Dihedral : 9.555 85.235 1296 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.92 % Allowed : 18.40 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.20 (0.26), residues: 1026 helix: 2.16 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.08 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 602 TYR 0.010 0.001 TYR C 824 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8552) covalent geometry : angle 0.49280 / 0.25 (11621) hydrogen bonds : bond 0.04211 / 2.85 ( 560) hydrogen bonds : angle 4.25479 / 3.12 ( 1617) link_BETA1-4 : bond 0.00268 / 0.18 ( 1) link_BETA1-4 : angle 1.12937 / 0.84 ( 3) link_BETA1-6 : bond 0.00368 / 0.25 ( 1) link_BETA1-6 : angle 1.34505 / 1.07 ( 3) link_NAG-ASN : bond 0.00179 / 0.12 ( 2) link_NAG-ASN : angle 1.14688 / 0.84 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: C 729 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7940 (t) REVERT: C 759 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7067 (pp30) REVERT: B 392 TYR cc_start: 0.7627 (m-80) cc_final: 0.7278 (m-80) REVERT: B 853 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (t) outliers start: 17 outliers final: 14 residues processed: 64 average time/residue: 0.1435 time to fit residues: 15.0657 Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 665 PHE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0670 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.089151 restraints weight = 49242.818| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.11 r_work: 0.3337 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8556 Z= 0.125 Angle : 0.487 5.074 11633 Z= 0.245 Chirality : 0.038 0.161 1388 Planarity : 0.004 0.044 1395 Dihedral : 9.305 86.089 1296 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.03 % Allowed : 18.28 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.27 (0.26), residues: 1026 helix: 2.21 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.11 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 602 TYR 0.010 0.001 TYR C 824 PHE 0.013 0.001 PHE B 471 TRP 0.011 0.001 TRP C 492 HIS 0.003 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8552) covalent geometry : angle 0.48599 / 0.24 (11621) hydrogen bonds : bond 0.04111 / 2.78 ( 560) hydrogen bonds : angle 4.19798 / 3.08 ( 1617) link_BETA1-4 : bond 0.00322 / 0.21 ( 1) link_BETA1-4 : angle 1.16781 / 0.88 ( 3) link_BETA1-6 : bond 0.00453 / 0.30 ( 1) link_BETA1-6 : angle 1.31425 / 1.04 ( 3) link_NAG-ASN : bond 0.00181 / 0.12 ( 2) link_NAG-ASN : angle 1.11485 / 0.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.22 seconds wall clock time: 69 minutes 17.03 seconds (4157.03 seconds total)