Starting phenix.real_space_refine on Thu Jul 2 08:19:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t44_41019/07_2026/8t44_41019.map" } resolution = 3.12 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= 0.063 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 9 5.49 5 S 34 5.16 5 C 5224 2.51 5 N 1203 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 7794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3525 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 420} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4037 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 142 Unusual residues: {'NAG': 1, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {'CO3': 1, 'NAG': 1, 'PLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.19 Number of scatterers: 7794 At special positions: 0 Unit cell: (84.53, 72.76, 128.4, 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 34 16.00 P 9 15.00 O 1324 8.00 N 1203 7.00 C 5224 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 A1001 " - " ASN A 642 " " NAG B1002 " - " ASN B 642 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 335.7 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 77.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 406 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 removed outlier: 3.507A pdb=" N VAL A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.612A pdb=" N VAL A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 594 removed outlier: 3.741A 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 624 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 684 Processing helix chain 'A' and resid 704 through 719 removed outlier: 3.818A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 773 Processing helix chain 'A' and resid 776 through 783 Processing helix chain 'A' and resid 784 through 800 removed outlier: 3.984A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 removed outlier: 3.525A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.589A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.754A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 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 removed outlier: 3.545A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (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 507 Processing helix chain 'B' and resid 508 through 516 Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 594 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 702 through 719 removed outlier: 3.850A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 800 removed outlier: 3.686A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 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 removed outlier: 3.519A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 6.906A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 727 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 725 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA3, first strand: chain 'B' and resid 739 through 740 518 hydrogen bonds defined for protein. 1506 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: 1.08 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1130 1.30 - 1.43: 2085 1.43 - 1.56: 4693 1.56 - 1.69: 14 1.69 - 1.82: 62 Bond restraints: 7984 Sorted by residual: bond pdb=" CB PLC B1004 " pdb=" O3 PLC B1004 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C' PLC B1004 " pdb=" O2 PLC B1004 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" CB PLC A1004 " pdb=" O3 PLC A1004 " ideal model delta sigma weight residual 1.327 1.449 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C' PLC A1004 " pdb=" O2 PLC A1004 " ideal model delta sigma weight residual 1.332 1.450 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C GLU B 681 " pdb=" O GLU B 681 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.66e+01 ... (remaining 7979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 10626 2.75 - 5.51: 164 5.51 - 8.26: 28 8.26 - 11.02: 17 11.02 - 13.77: 2 Bond angle restraints: 10837 Sorted by residual: angle pdb=" N SER B 801 " pdb=" CA SER B 801 " pdb=" C SER B 801 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.60e+01 angle pdb=" N THR B 728 " pdb=" CA THR B 728 " pdb=" C THR B 728 " ideal model delta sigma weight residual 111.07 119.57 -8.50 1.07e+00 8.73e-01 6.31e+01 angle pdb=" O11 PIO A1003 " pdb=" P1 PIO A1003 " pdb=" O12 PIO A1003 " ideal model delta sigma weight residual 121.09 107.32 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CA GLU B 681 " pdb=" C GLU B 681 " pdb=" N SER B 682 " ideal model delta sigma weight residual 116.92 121.54 -4.62 1.16e+00 7.43e-01 1.59e+01 angle pdb=" O11 PIO A1002 " pdb=" P1 PIO A1002 " pdb=" O12 PIO A1002 " ideal model delta sigma weight residual 121.09 110.01 11.08 3.00e+00 1.11e-01 1.36e+01 ... (remaining 10832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 4435 28.17 - 56.33: 240 56.33 - 84.50: 33 84.50 - 112.66: 13 112.66 - 140.83: 7 Dihedral angle restraints: 4728 sinusoidal: 1969 harmonic: 2759 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 -73.67 140.83 1 3.00e+01 1.11e-03 1.89e+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 304.29 164.21 140.08 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C2' PLC B1003 " pdb=" C' PLC B1003 " pdb=" C1' PLC B1003 " pdb=" O' PLC B1003 " ideal model delta sinusoidal sigma weight residual -11.03 116.94 -127.97 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 4725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1085 0.057 - 0.113: 179 0.113 - 0.170: 17 0.170 - 0.226: 3 0.226 - 0.283: 4 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA SER B 801 " pdb=" N SER B 801 " pdb=" C SER B 801 " pdb=" CB SER B 801 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2 PLC A1004 " pdb=" C1 PLC A1004 " pdb=" C3 PLC A1004 " pdb=" O2 PLC A1004 " both_signs ideal model delta sigma weight residual False -2.31 -2.58 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 PLC B1004 " pdb=" C1 PLC B1004 " pdb=" C3 PLC B1004 " pdb=" O2 PLC B1004 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1285 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CO3 B1001 " 0.071 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" O1 CO3 B1001 " -0.025 2.00e-02 2.50e+03 pdb=" O2 CO3 B1001 " -0.023 2.00e-02 2.50e+03 pdb=" O3 CO3 B1001 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 514 " -0.141 9.50e-02 1.11e+02 6.34e-02 2.66e+00 pdb=" NE ARG B 514 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 514 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 514 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 514 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 390 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 391 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 391 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 391 " 0.022 5.00e-02 4.00e+02 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2282 2.82 - 3.34: 7997 3.34 - 3.86: 12985 3.86 - 4.38: 15246 4.38 - 4.90: 25984 Nonbonded interactions: 64494 Sorted by model distance: nonbonded pdb=" N GLY B 381 " pdb=" OE2 GLU B 508 " model vdw 2.301 3.120 nonbonded pdb=" OE1 GLN B 457 " pdb=" OG SER B 690 " model vdw 2.301 3.040 nonbonded pdb=" O ALA A 452 " pdb=" NE ARG A 760 " model vdw 2.337 3.120 nonbonded pdb=" O ASP A 887 " pdb=" OD1 ASP A 887 " model vdw 2.347 3.040 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.383 3.040 ... (remaining 64489 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 406 through 888 or (resid 889 and (name N or name CA or na \ me C or name O or name CB )) or (resid 1004 and (name CB or name OB or name C' o \ r 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 C8B or name C9' or n \ ame C9B or name CA' or name CAA or name CB' or name CBA or name O' or name O1P o \ r name O2 or name O2P or name O3 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 406 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 685 or resid 703 through 729 o \ r resid 752 through 889 or resid 1004)) } 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: 2.260 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.970 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.005 0.124 7986 Z= 0.267 Angle : 0.873 13.775 10843 Z= 0.399 Chirality : 0.042 0.283 1288 Planarity : 0.005 0.063 1297 Dihedral : 18.540 140.827 2946 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.48 % Allowed : 16.67 % Favored : 82.85 % 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: 1.84 (0.28), residues: 947 helix: 1.90 (0.20), residues: 677 sheet: None (None), residues: 0 loop : -0.50 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.012 0.001 TYR A 486 PHE 0.016 0.001 PHE A 471 TRP 0.019 0.001 TRP B 492 HIS 0.001 0.000 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.27 ( 7984) covalent geometry : angle 0.85873 / 0.40 (10837) hydrogen bonds : bond 0.12383 / 8.44 ( 518) hydrogen bonds : angle 4.93044 / 3.71 ( 1506) link_NAG-ASN : bond 0.00726 / 0.38 ( 2) link_NAG-ASN : angle 6.67441 / 2.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.196 Fit side-chains REVERT: A 430 LYS cc_start: 0.8133 (mttp) cc_final: 0.7903 (tptp) REVERT: A 818 TYR cc_start: 0.7280 (m-80) cc_final: 0.6947 (m-80) outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 0.0670 time to fit residues: 11.0756 Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3701 r_free = 0.3701 target = 0.150670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129767 restraints weight = 10198.581| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.61 r_work: 0.3345 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7986 Z= 0.131 Angle : 0.587 13.343 10843 Z= 0.284 Chirality : 0.041 0.198 1288 Planarity : 0.005 0.047 1297 Dihedral : 14.907 130.532 1188 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.64 % Allowed : 16.43 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.27), residues: 947 helix: 1.99 (0.20), residues: 681 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 827 TYR 0.012 0.001 TYR B 553 PHE 0.017 0.001 PHE A 471 TRP 0.014 0.001 TRP B 492 HIS 0.002 0.000 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7984) covalent geometry : angle 0.56716 / 0.28 (10837) hydrogen bonds : bond 0.04402 / 2.93 ( 518) hydrogen bonds : angle 4.29366 / 3.12 ( 1506) link_NAG-ASN : bond 0.00755 / 0.40 ( 2) link_NAG-ASN : angle 6.52015 / 2.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.185 Fit side-chains REVERT: A 818 TYR cc_start: 0.7389 (m-80) cc_final: 0.7019 (m-80) REVERT: B 435 MET cc_start: 0.8274 (ttp) cc_final: 0.8066 (ttp) REVERT: B 588 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 643 SER cc_start: 0.8507 (t) cc_final: 0.8070 (p) outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 0.0562 time to fit residues: 10.4130 Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 569 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126937 restraints weight = 10255.909| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.62 r_work: 0.3295 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7986 Z= 0.153 Angle : 0.584 11.065 10843 Z= 0.280 Chirality : 0.042 0.189 1288 Planarity : 0.005 0.048 1297 Dihedral : 13.296 110.058 1186 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.76 % Allowed : 17.63 % Favored : 79.62 % 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: 1.77 (0.27), residues: 947 helix: 1.90 (0.20), residues: 681 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.017 0.002 TYR B 824 PHE 0.024 0.001 PHE A 659 TRP 0.013 0.001 TRP B 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7984) covalent geometry : angle 0.56945 / 0.28 (10837) hydrogen bonds : bond 0.04385 / 2.96 ( 518) hydrogen bonds : angle 4.23358 / 3.09 ( 1506) link_NAG-ASN : bond 0.00514 / 0.27 ( 2) link_NAG-ASN : angle 5.54990 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 818 TYR cc_start: 0.7395 (m-80) cc_final: 0.7112 (m-80) REVERT: B 399 ASP cc_start: 0.8352 (t0) cc_final: 0.8124 (t0) REVERT: B 588 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 681 GLU cc_start: 0.7627 (tt0) cc_final: 0.7399 (tp30) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.0656 time to fit residues: 12.3367 Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 759 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128529 restraints weight = 10393.215| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.61 r_work: 0.3348 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7986 Z= 0.125 Angle : 0.547 9.896 10843 Z= 0.264 Chirality : 0.040 0.200 1288 Planarity : 0.005 0.049 1297 Dihedral : 12.506 90.614 1186 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.36 % Allowed : 16.67 % Favored : 79.98 % 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: 1.82 (0.27), residues: 947 helix: 1.96 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.77 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 603 TYR 0.014 0.001 TYR B 824 PHE 0.020 0.001 PHE A 659 TRP 0.014 0.001 TRP B 492 HIS 0.002 0.000 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7984) covalent geometry : angle 0.53365 / 0.26 (10837) hydrogen bonds : bond 0.04042 / 2.72 ( 518) hydrogen bonds : angle 4.15472 / 3.03 ( 1506) link_NAG-ASN : bond 0.00446 / 0.23 ( 2) link_NAG-ASN : angle 5.13050 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 818 TYR cc_start: 0.7393 (m-80) cc_final: 0.7110 (m-80) REVERT: B 588 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8052 (mm) REVERT: B 681 GLU cc_start: 0.7561 (tt0) cc_final: 0.7324 (tp30) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.0616 time to fit residues: 11.2989 Evaluate side-chains 125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.0470 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3697 r_free = 0.3697 target = 0.149988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129068 restraints weight = 10324.441| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.63 r_work: 0.3361 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7986 Z= 0.110 Angle : 0.527 9.065 10843 Z= 0.254 Chirality : 0.040 0.201 1288 Planarity : 0.005 0.049 1297 Dihedral : 11.878 87.651 1186 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.12 % Allowed : 17.03 % Favored : 79.86 % 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: 1.92 (0.27), residues: 947 helix: 2.04 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.76 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.013 0.001 TYR B 824 PHE 0.015 0.001 PHE B 471 TRP 0.012 0.001 TRP B 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7984) covalent geometry : angle 0.51538 / 0.25 (10837) hydrogen bonds : bond 0.03868 / 2.60 ( 518) hydrogen bonds : angle 4.08675 / 2.98 ( 1506) link_NAG-ASN : bond 0.00429 / 0.22 ( 2) link_NAG-ASN : angle 4.75834 / 2.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8456 (tpp) cc_final: 0.7552 (tpp) REVERT: A 818 TYR cc_start: 0.7306 (m-80) cc_final: 0.7017 (m-80) REVERT: B 588 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8033 (mm) REVERT: B 681 GLU cc_start: 0.7518 (tt0) cc_final: 0.7284 (tp30) REVERT: B 721 MET cc_start: 0.8237 (mmm) cc_final: 0.7632 (mmt) outliers start: 26 outliers final: 19 residues processed: 129 average time/residue: 0.0585 time to fit residues: 10.8475 Evaluate side-chains 125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 759 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130663 restraints weight = 10224.048| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.66 r_work: 0.3358 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7986 Z= 0.113 Angle : 0.521 8.243 10843 Z= 0.252 Chirality : 0.040 0.206 1288 Planarity : 0.005 0.049 1297 Dihedral : 10.785 88.668 1186 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.72 % Allowed : 17.15 % Favored : 79.14 % 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: 1.93 (0.27), residues: 947 helix: 2.07 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.011 0.001 TYR B 824 PHE 0.015 0.001 PHE B 471 TRP 0.014 0.001 TRP B 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7984) covalent geometry : angle 0.51113 / 0.25 (10837) hydrogen bonds : bond 0.03818 / 2.57 ( 518) hydrogen bonds : angle 4.01862 / 2.94 ( 1506) link_NAG-ASN : bond 0.00332 / 0.17 ( 2) link_NAG-ASN : angle 4.42867 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8389 (tpp) cc_final: 0.7502 (tpp) REVERT: A 640 VAL cc_start: 0.7499 (m) cc_final: 0.7219 (t) REVERT: A 664 MET cc_start: 0.6762 (ttm) cc_final: 0.6552 (ttm) REVERT: A 818 TYR cc_start: 0.7267 (m-80) cc_final: 0.6993 (m-80) REVERT: B 433 ASN cc_start: 0.8855 (t0) cc_final: 0.8475 (t0) REVERT: B 588 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 643 SER cc_start: 0.8505 (t) cc_final: 0.8046 (p) REVERT: B 681 GLU cc_start: 0.7501 (tt0) cc_final: 0.7268 (tp30) outliers start: 31 outliers final: 20 residues processed: 142 average time/residue: 0.0615 time to fit residues: 12.6906 Evaluate side-chains 128 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 91 optimal weight: 0.0170 chunk 88 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 754 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130214 restraints weight = 10253.076| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.63 r_work: 0.3362 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7986 Z= 0.114 Angle : 0.523 7.733 10843 Z= 0.252 Chirality : 0.040 0.209 1288 Planarity : 0.005 0.049 1297 Dihedral : 10.321 83.193 1186 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.24 % Allowed : 18.59 % Favored : 78.18 % 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: 947 helix: 2.08 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.76 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 514 TYR 0.011 0.001 TYR A 824 PHE 0.015 0.001 PHE B 471 TRP 0.012 0.001 TRP B 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7984) covalent geometry : angle 0.51402 / 0.25 (10837) hydrogen bonds : bond 0.03777 / 2.54 ( 518) hydrogen bonds : angle 4.01748 / 2.94 ( 1506) link_NAG-ASN : bond 0.00300 / 0.16 ( 2) link_NAG-ASN : angle 4.19738 / 1.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8392 (tpp) cc_final: 0.7529 (tpp) REVERT: A 640 VAL cc_start: 0.7510 (m) cc_final: 0.7226 (t) REVERT: A 818 TYR cc_start: 0.7284 (m-80) cc_final: 0.7007 (m-80) REVERT: B 433 ASN cc_start: 0.8833 (t0) cc_final: 0.8461 (t0) REVERT: B 558 LEU cc_start: 0.7270 (mp) cc_final: 0.7036 (mt) REVERT: B 588 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8031 (mm) REVERT: B 643 SER cc_start: 0.8506 (t) cc_final: 0.8033 (p) outliers start: 27 outliers final: 21 residues processed: 126 average time/residue: 0.0661 time to fit residues: 11.9410 Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 545 GLN B 754 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127143 restraints weight = 10328.173| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.65 r_work: 0.3312 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7986 Z= 0.153 Angle : 0.558 7.741 10843 Z= 0.271 Chirality : 0.041 0.211 1288 Planarity : 0.005 0.048 1297 Dihedral : 10.187 84.470 1186 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.72 % Allowed : 18.59 % Favored : 77.70 % 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: 1.79 (0.27), residues: 947 helix: 1.93 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.77 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 514 TYR 0.012 0.001 TYR B 519 PHE 0.015 0.001 PHE B 471 TRP 0.014 0.002 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7984) covalent geometry : angle 0.54956 / 0.27 (10837) hydrogen bonds : bond 0.04093 / 2.74 ( 518) hydrogen bonds : angle 4.11826 / 3.01 ( 1506) link_NAG-ASN : bond 0.00262 / 0.14 ( 2) link_NAG-ASN : angle 4.18123 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 640 VAL cc_start: 0.7582 (m) cc_final: 0.7288 (t) REVERT: A 818 TYR cc_start: 0.7290 (m-80) cc_final: 0.7001 (m-80) REVERT: B 433 ASN cc_start: 0.8965 (t0) cc_final: 0.8631 (t0) REVERT: B 588 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8030 (mm) REVERT: B 681 GLU cc_start: 0.7454 (tt0) cc_final: 0.7227 (tp30) REVERT: B 774 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8307 (mt) outliers start: 31 outliers final: 24 residues processed: 127 average time/residue: 0.0624 time to fit residues: 11.5254 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128845 restraints weight = 10291.870| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.64 r_work: 0.3332 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7986 Z= 0.121 Angle : 0.537 7.447 10843 Z= 0.261 Chirality : 0.041 0.212 1288 Planarity : 0.005 0.049 1297 Dihedral : 9.769 85.192 1186 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.24 % Allowed : 18.82 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 947 helix: 2.00 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.018 0.001 TYR B 824 PHE 0.015 0.001 PHE B 471 TRP 0.014 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7984) covalent geometry : angle 0.52853 / 0.26 (10837) hydrogen bonds : bond 0.03875 / 2.61 ( 518) hydrogen bonds : angle 4.07573 / 2.99 ( 1506) link_NAG-ASN : bond 0.00254 / 0.13 ( 2) link_NAG-ASN : angle 4.04338 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8360 (tpp) cc_final: 0.7477 (tpp) REVERT: A 640 VAL cc_start: 0.7537 (m) cc_final: 0.7252 (t) REVERT: A 818 TYR cc_start: 0.7278 (m-80) cc_final: 0.7041 (m-80) REVERT: B 433 ASN cc_start: 0.8952 (t0) cc_final: 0.8645 (t0) REVERT: B 588 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 681 GLU cc_start: 0.7564 (tt0) cc_final: 0.7341 (tp30) REVERT: B 774 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8274 (mt) outliers start: 27 outliers final: 23 residues processed: 125 average time/residue: 0.0645 time to fit residues: 11.6008 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3694 r_free = 0.3694 target = 0.149567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128365 restraints weight = 10244.127| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.66 r_work: 0.3331 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7986 Z= 0.118 Angle : 0.529 7.272 10843 Z= 0.258 Chirality : 0.041 0.213 1288 Planarity : 0.005 0.049 1297 Dihedral : 9.536 86.554 1186 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.24 % Allowed : 19.06 % Favored : 77.70 % 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: 1.90 (0.27), residues: 947 helix: 2.01 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 432 TYR 0.016 0.001 TYR B 824 PHE 0.015 0.001 PHE B 471 TRP 0.019 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7984) covalent geometry : angle 0.52107 / 0.26 (10837) hydrogen bonds : bond 0.03845 / 2.58 ( 518) hydrogen bonds : angle 4.05191 / 2.98 ( 1506) link_NAG-ASN : bond 0.00235 / 0.12 ( 2) link_NAG-ASN : angle 3.89367 / 1.71 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8367 (tpp) cc_final: 0.7493 (tpp) REVERT: A 640 VAL cc_start: 0.7536 (m) cc_final: 0.7244 (t) REVERT: A 818 TYR cc_start: 0.7282 (m-80) cc_final: 0.7038 (m-80) REVERT: B 433 ASN cc_start: 0.8975 (t0) cc_final: 0.8676 (t0) REVERT: B 588 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8026 (mm) REVERT: B 681 GLU cc_start: 0.7542 (tt0) cc_final: 0.7292 (tp30) REVERT: B 774 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8266 (mt) outliers start: 27 outliers final: 23 residues processed: 127 average time/residue: 0.0630 time to fit residues: 11.5882 Evaluate side-chains 131 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 723 TRP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3711 r_free = 0.3711 target = 0.151067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130090 restraints weight = 10246.035| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.63 r_work: 0.3361 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7986 Z= 0.109 Angle : 0.525 7.076 10843 Z= 0.256 Chirality : 0.040 0.215 1288 Planarity : 0.005 0.049 1297 Dihedral : 9.311 88.323 1186 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.36 % Allowed : 18.82 % Favored : 77.82 % 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: 1.98 (0.27), residues: 947 helix: 2.06 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.67 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.017 0.001 TYR B 824 PHE 0.016 0.001 PHE B 401 TRP 0.021 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7984) covalent geometry : angle 0.51812 / 0.25 (10837) hydrogen bonds : bond 0.03737 / 2.51 ( 518) hydrogen bonds : angle 4.02056 / 2.96 ( 1506) link_NAG-ASN : bond 0.00229 / 0.12 ( 2) link_NAG-ASN : angle 3.71064 / 1.63 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.42 seconds wall clock time: 26 minutes 28.68 seconds (1588.68 seconds total)