Starting phenix.real_space_refine on Thu Jul 2 06:45:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3u_41012/07_2026/8t3u_41012.cif" } resolution = 2.97 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= 0.077 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 8 5.49 5 S 31 5.16 5 C 4920 2.51 5 N 1123 2.21 5 O 1238 1.98 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: 7320 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3575 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3555 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.68, per 1000 atoms: 0.23 Number of scatterers: 7320 At special positions: 0 Unit cell: (96.12, 117.72, 84.24, 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 31 16.00 P 8 15.00 O 1238 8.00 N 1123 7.00 C 4920 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 B1003 " - " ASN B 642 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 361.5 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 76.4% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 removed outlier: 4.636A pdb=" N ILE A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.623A pdb=" N ARG A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.749A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 687 Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.667A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.819A 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 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.619A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.816A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.502A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.581A 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 404 through 431 removed outlier: 3.752A pdb=" N ILE B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 412 " --> pdb=" O ALA B 408 " (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 removed outlier: 3.674A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.806A pdb=" N LEU B 512 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.511A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 623 Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 686 Processing helix chain 'B' and resid 703 through 719 removed outlier: 3.729A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.613A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.908A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.787A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 873 removed outlier: 3.569A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.725A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.540A pdb=" N CYS B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 460 through 463 Processing sheet with id=AA2, first strand: chain 'B' and resid 461 through 463 478 hydrogen bonds defined for protein. 1410 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: 1.14 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1063 1.31 - 1.43: 2004 1.43 - 1.56: 4367 1.56 - 1.68: 12 1.68 - 1.81: 56 Bond restraints: 7502 Sorted by residual: bond pdb=" C1A PIO B1001 " pdb=" O2C PIO B1001 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1B PIO A1003 " pdb=" O3C PIO A1003 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1B PIO B1001 " pdb=" O3C PIO B1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1A PIO A1003 " pdb=" O2C PIO A1003 " ideal model delta sigma weight residual 1.332 1.397 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O4 PIO A1003 " pdb=" P4 PIO A1003 " ideal model delta sigma weight residual 1.710 1.647 0.063 2.00e-02 2.50e+03 9.96e+00 ... (remaining 7497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 10004 2.53 - 5.06: 148 5.06 - 7.60: 33 7.60 - 10.13: 7 10.13 - 12.66: 4 Bond angle restraints: 10196 Sorted by residual: angle pdb=" C PHE A 597 " pdb=" N PRO A 598 " pdb=" CA PRO A 598 " ideal model delta sigma weight residual 119.78 114.15 5.63 1.03e+00 9.43e-01 2.99e+01 angle pdb=" O11 PIO B1001 " pdb=" P1 PIO B1001 " pdb=" O12 PIO B1001 " ideal model delta sigma weight residual 121.09 108.43 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O1 PIO A1003 " pdb=" P1 PIO A1003 " pdb=" O13 PIO A1003 " ideal model delta sigma weight residual 97.64 109.64 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1 PIO B1001 " pdb=" P1 PIO B1001 " pdb=" O13 PIO B1001 " ideal model delta sigma weight residual 97.64 109.61 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O11 PIO A1003 " pdb=" P1 PIO A1003 " pdb=" O12 PIO A1003 " ideal model delta sigma weight residual 121.09 109.12 11.97 3.00e+00 1.11e-01 1.59e+01 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.25: 4243 27.25 - 54.49: 158 54.49 - 81.74: 16 81.74 - 108.99: 1 108.99 - 136.23: 4 Dihedral angle restraints: 4422 sinusoidal: 1810 harmonic: 2612 Sorted by residual: dihedral pdb=" C2' PLC B1002 " pdb=" C' PLC B1002 " pdb=" C1' PLC B1002 " pdb=" O' PLC B1002 " ideal model delta sinusoidal sigma weight residual -11.03 125.20 -136.23 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C2' PLC B1002 " pdb=" C' PLC B1002 " pdb=" C1' PLC B1002 " pdb=" O2 PLC B1002 " ideal model delta sinusoidal sigma weight residual 169.53 -54.35 -136.12 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3 PLC B1002 " pdb=" C1 PLC B1002 " pdb=" C2 PLC B1002 " pdb=" O3P PLC B1002 " ideal model delta sinusoidal sigma weight residual 67.16 -52.11 119.27 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 4419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 894 0.045 - 0.090: 263 0.090 - 0.134: 60 0.134 - 0.179: 6 0.179 - 0.224: 1 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA PHE A 597 " pdb=" N PHE A 597 " pdb=" C PHE A 597 " pdb=" CB PHE A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2C PIO B1001 " pdb=" C1C PIO B1001 " pdb=" C3C PIO B1001 " pdb=" O2C PIO B1001 " both_signs ideal model delta sigma weight residual False -2.56 -2.39 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C1 PIO A1003 " pdb=" C2 PIO A1003 " pdb=" C6 PIO A1003 " pdb=" O1 PIO A1003 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 1221 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 597 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO B 598 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 874 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO B 875 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 875 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 875 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 874 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 875 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 875 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 875 " 0.024 5.00e-02 4.00e+02 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1260 2.77 - 3.30: 6952 3.30 - 3.83: 12125 3.83 - 4.37: 13700 4.37 - 4.90: 24600 Nonbonded interactions: 58637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 472 " pdb=" OH TYR A 486 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.268 3.040 nonbonded pdb=" O PRO A 568 " pdb=" ND2 ASN B 569 " model vdw 2.297 3.120 nonbonded pdb=" NH2 ARG A 808 " pdb=" OE1 GLN A 840 " model vdw 2.333 3.120 nonbonded pdb=" O LEU A 863 " pdb=" OG1 THR A 866 " model vdw 2.343 3.040 ... (remaining 58632 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 404 and (name N or name CA or name C or name O or name CB \ )) or resid 405 through 687 or resid 702 through 728 or resid 753 through 890 o \ r (resid 1002 and (name CB or name OB or name C' or name C1 or name C1' or name \ C1B or name C2 or name C2' or name C2B or name C3 or name C3' or name C3B or nam \ e 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 name C9B or name CA' or name CA \ A or name CB' or name CBA or name O' or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 404 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 663 or (resid 664 and (name N \ or name CA or name C or name O or name CB )) or resid 665 through 686 or (resid \ 687 and (name N or name CA or name C or name O or name CB )) or resid 702 throug \ h 890 or resid 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.000 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7504 Z= 0.208 Angle : 0.793 12.662 10202 Z= 0.365 Chirality : 0.043 0.224 1224 Planarity : 0.005 0.049 1216 Dihedral : 14.312 136.234 2732 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.28), residues: 894 helix: 1.61 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 589 TYR 0.015 0.002 TYR B 486 PHE 0.012 0.001 PHE A 495 TRP 0.020 0.002 TRP B 723 HIS 0.007 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 ( 7502) covalent geometry : angle 0.79221 / 0.37 (10196) hydrogen bonds : bond 0.12822 / 9.22 ( 478) hydrogen bonds : angle 4.95121 / 3.46 ( 1410) link_NAG-ASN : bond 0.00215 / 0.11 ( 2) link_NAG-ASN : angle 1.24378 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.222 Fit side-chains REVERT: A 590 LYS cc_start: 0.8246 (ttmm) cc_final: 0.8022 (ttmm) REVERT: B 413 TYR cc_start: 0.8249 (t80) cc_final: 0.8011 (t80) REVERT: B 887 ASP cc_start: 0.8714 (t0) cc_final: 0.8443 (t0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.5074 time to fit residues: 76.0557 Evaluate side-chains 97 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN B 482 ASN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118642 restraints weight = 8262.427| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.82 r_work: 0.3150 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7504 Z= 0.128 Angle : 0.543 7.906 10202 Z= 0.262 Chirality : 0.041 0.216 1224 Planarity : 0.005 0.041 1216 Dihedral : 10.103 108.877 1092 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.92 % Allowed : 10.61 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.28), residues: 894 helix: 1.77 (0.21), residues: 629 sheet: None (None), residues: 0 loop : -0.83 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.015 0.001 TYR B 486 PHE 0.015 0.001 PHE A 476 TRP 0.010 0.001 TRP B 723 HIS 0.005 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7502) covalent geometry : angle 0.54194 / 0.26 (10196) hydrogen bonds : bond 0.04588 / 3.12 ( 478) hydrogen bonds : angle 4.09480 / 2.86 ( 1410) link_NAG-ASN : bond 0.00279 / 0.14 ( 2) link_NAG-ASN : angle 1.16576 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.259 Fit side-chains REVERT: A 457 GLN cc_start: 0.6785 (tp-100) cc_final: 0.6462 (tp-100) REVERT: A 485 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 590 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7797 (ttmm) REVERT: B 721 MET cc_start: 0.8139 (mpp) cc_final: 0.7729 (mpp) outliers start: 15 outliers final: 7 residues processed: 115 average time/residue: 0.4151 time to fit residues: 50.7178 Evaluate side-chains 107 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117460 restraints weight = 8242.051| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.90 r_work: 0.3120 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7504 Z= 0.130 Angle : 0.529 6.690 10202 Z= 0.255 Chirality : 0.041 0.204 1224 Planarity : 0.005 0.042 1216 Dihedral : 8.971 82.009 1092 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.94 % Allowed : 12.79 % Favored : 84.27 % 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: 1.71 (0.28), residues: 894 helix: 1.89 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.013 0.002 TYR A 824 PHE 0.018 0.001 PHE A 476 TRP 0.008 0.001 TRP B 492 HIS 0.004 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7502) covalent geometry : angle 0.52832 / 0.26 (10196) hydrogen bonds : bond 0.04456 / 3.03 ( 478) hydrogen bonds : angle 3.95328 / 2.78 ( 1410) link_NAG-ASN : bond 0.00339 / 0.17 ( 2) link_NAG-ASN : angle 1.24089 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.171 Fit side-chains REVERT: A 457 GLN cc_start: 0.6824 (tp-100) cc_final: 0.6508 (tp40) REVERT: A 485 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: A 553 TYR cc_start: 0.9275 (m-80) cc_final: 0.8878 (m-80) REVERT: A 559 MET cc_start: 0.8436 (mmm) cc_final: 0.7723 (mmt) REVERT: A 590 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7720 (ttmm) REVERT: A 721 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: B 435 MET cc_start: 0.7678 (mtp) cc_final: 0.7453 (mtm) REVERT: B 590 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7751 (ttmm) REVERT: B 721 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 887 ASP cc_start: 0.8470 (t0) cc_final: 0.8264 (t0) outliers start: 23 outliers final: 9 residues processed: 116 average time/residue: 0.4284 time to fit residues: 52.6798 Evaluate side-chains 112 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 ASN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115789 restraints weight = 8404.679| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.81 r_work: 0.3105 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7504 Z= 0.142 Angle : 0.531 6.364 10202 Z= 0.258 Chirality : 0.041 0.211 1224 Planarity : 0.005 0.041 1216 Dihedral : 8.594 69.840 1092 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.32 % Allowed : 14.58 % Favored : 82.10 % 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: 1.68 (0.28), residues: 894 helix: 1.85 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 603 TYR 0.013 0.002 TYR A 824 PHE 0.013 0.001 PHE B 471 TRP 0.010 0.001 TRP B 492 HIS 0.005 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 7502) covalent geometry : angle 0.53059 / 0.26 (10196) hydrogen bonds : bond 0.04541 / 3.07 ( 478) hydrogen bonds : angle 3.92268 / 2.77 ( 1410) link_NAG-ASN : bond 0.00328 / 0.16 ( 2) link_NAG-ASN : angle 1.26679 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.269 Fit side-chains REVERT: A 457 GLN cc_start: 0.6786 (tp-100) cc_final: 0.6443 (tp-100) REVERT: A 485 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: A 553 TYR cc_start: 0.9284 (m-80) cc_final: 0.8949 (m-80) REVERT: A 559 MET cc_start: 0.8484 (mmm) cc_final: 0.7707 (mmt) REVERT: A 590 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7678 (ttmm) REVERT: A 721 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: B 435 MET cc_start: 0.7680 (mtp) cc_final: 0.7457 (mtm) REVERT: B 590 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7713 (ttmm) REVERT: B 721 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: B 887 ASP cc_start: 0.8485 (t0) cc_final: 0.8224 (t0) outliers start: 26 outliers final: 12 residues processed: 111 average time/residue: 0.4622 time to fit residues: 54.4350 Evaluate side-chains 109 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 648 TRP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117104 restraints weight = 8248.781| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.80 r_work: 0.3133 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7504 Z= 0.117 Angle : 0.502 6.241 10202 Z= 0.244 Chirality : 0.040 0.206 1224 Planarity : 0.005 0.040 1216 Dihedral : 8.445 77.110 1092 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.58 % Allowed : 15.35 % Favored : 81.07 % 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: 1.89 (0.28), residues: 894 helix: 2.01 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 603 TYR 0.011 0.001 TYR B 486 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP B 492 HIS 0.003 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7502) covalent geometry : angle 0.50118 / 0.24 (10196) hydrogen bonds : bond 0.04213 / 2.85 ( 478) hydrogen bonds : angle 3.82079 / 2.70 ( 1410) link_NAG-ASN : bond 0.00316 / 0.16 ( 2) link_NAG-ASN : angle 1.25883 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.216 Fit side-chains REVERT: A 457 GLN cc_start: 0.6799 (tp-100) cc_final: 0.6426 (tp-100) REVERT: A 485 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 553 TYR cc_start: 0.9278 (m-80) cc_final: 0.8972 (m-80) REVERT: A 559 MET cc_start: 0.8505 (mmm) cc_final: 0.7726 (mmt) REVERT: A 590 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7663 (ttmm) REVERT: A 721 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: B 553 TYR cc_start: 0.9209 (m-80) cc_final: 0.8992 (m-80) REVERT: B 589 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7486 (ttm170) REVERT: B 590 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7747 (ttmm) REVERT: B 721 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7813 (mpp) REVERT: B 887 ASP cc_start: 0.8407 (t0) cc_final: 0.8136 (t0) outliers start: 28 outliers final: 14 residues processed: 116 average time/residue: 0.4683 time to fit residues: 57.5138 Evaluate side-chains 114 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117234 restraints weight = 8300.342| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.88 r_work: 0.3112 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7504 Z= 0.124 Angle : 0.504 6.285 10202 Z= 0.246 Chirality : 0.040 0.211 1224 Planarity : 0.005 0.041 1216 Dihedral : 8.416 85.443 1092 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.22 % Allowed : 15.09 % Favored : 80.69 % 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 (0.29), residues: 894 helix: 2.00 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.012 0.002 TYR B 413 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP B 492 HIS 0.004 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 7502) covalent geometry : angle 0.50352 / 0.25 (10196) hydrogen bonds : bond 0.04245 / 2.87 ( 478) hydrogen bonds : angle 3.81032 / 2.70 ( 1410) link_NAG-ASN : bond 0.00294 / 0.15 ( 2) link_NAG-ASN : angle 1.28771 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.345 Fit side-chains REVERT: A 457 GLN cc_start: 0.6765 (tp-100) cc_final: 0.6350 (tp-100) REVERT: A 485 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 553 TYR cc_start: 0.9269 (m-80) cc_final: 0.8902 (m-80) REVERT: A 559 MET cc_start: 0.8497 (mmm) cc_final: 0.7722 (mmt) REVERT: A 590 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7691 (ttmm) REVERT: A 721 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7965 (mtp) REVERT: B 553 TYR cc_start: 0.9228 (m-80) cc_final: 0.8994 (m-80) REVERT: B 589 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7367 (ttm170) REVERT: B 721 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7851 (mpp) REVERT: B 887 ASP cc_start: 0.8462 (t0) cc_final: 0.8178 (t0) outliers start: 33 outliers final: 18 residues processed: 117 average time/residue: 0.4948 time to fit residues: 61.3940 Evaluate side-chains 118 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115455 restraints weight = 8282.330| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.79 r_work: 0.3099 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7504 Z= 0.140 Angle : 0.524 6.355 10202 Z= 0.255 Chirality : 0.041 0.212 1224 Planarity : 0.005 0.040 1216 Dihedral : 8.229 77.422 1092 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.22 % Allowed : 15.22 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.28), residues: 894 helix: 1.91 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 879 TYR 0.013 0.002 TYR A 824 PHE 0.012 0.001 PHE B 471 TRP 0.010 0.001 TRP B 492 HIS 0.005 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 7502) covalent geometry : angle 0.52359 / 0.26 (10196) hydrogen bonds : bond 0.04458 / 3.01 ( 478) hydrogen bonds : angle 3.85101 / 2.72 ( 1410) link_NAG-ASN : bond 0.00314 / 0.16 ( 2) link_NAG-ASN : angle 1.32044 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.223 Fit side-chains REVERT: A 457 GLN cc_start: 0.6805 (tp-100) cc_final: 0.6412 (tp-100) REVERT: A 485 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 553 TYR cc_start: 0.9269 (m-80) cc_final: 0.8931 (m-80) REVERT: A 590 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7659 (ttmm) REVERT: A 675 PHE cc_start: 0.8695 (t80) cc_final: 0.8390 (t80) REVERT: A 721 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (mtp) REVERT: B 457 GLN cc_start: 0.6563 (tp-100) cc_final: 0.6342 (tp-100) REVERT: B 589 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7348 (ttm170) REVERT: B 663 MET cc_start: 0.8565 (tpt) cc_final: 0.8331 (mmm) REVERT: B 721 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7819 (mpp) REVERT: B 887 ASP cc_start: 0.8465 (t0) cc_final: 0.8209 (t0) outliers start: 33 outliers final: 18 residues processed: 120 average time/residue: 0.5268 time to fit residues: 66.6555 Evaluate side-chains 120 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.0010 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117484 restraints weight = 8325.727| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.81 r_work: 0.3126 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7504 Z= 0.109 Angle : 0.503 6.265 10202 Z= 0.242 Chirality : 0.039 0.206 1224 Planarity : 0.005 0.040 1216 Dihedral : 7.881 69.929 1092 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.58 % Allowed : 16.11 % Favored : 80.31 % 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 (0.29), residues: 894 helix: 2.06 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.60 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.012 0.001 TYR B 413 PHE 0.011 0.001 PHE B 471 TRP 0.013 0.001 TRP B 492 HIS 0.003 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7502) covalent geometry : angle 0.49735 / 0.24 (10196) hydrogen bonds : bond 0.04004 / 2.70 ( 478) hydrogen bonds : angle 3.75989 / 2.66 ( 1410) link_NAG-ASN : bond 0.00761 / 0.36 ( 2) link_NAG-ASN : angle 3.19721 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.189 Fit side-chains REVERT: A 457 GLN cc_start: 0.6682 (tp-100) cc_final: 0.6287 (tp-100) REVERT: A 485 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: A 553 TYR cc_start: 0.9261 (m-80) cc_final: 0.8924 (m-80) REVERT: A 590 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7588 (ttmm) REVERT: A 675 PHE cc_start: 0.8741 (t80) cc_final: 0.8409 (t80) REVERT: A 721 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: B 589 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: B 590 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7685 (ttmm) REVERT: B 663 MET cc_start: 0.8576 (tpt) cc_final: 0.8367 (mmm) REVERT: B 721 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: B 887 ASP cc_start: 0.8405 (t0) cc_final: 0.8161 (t0) outliers start: 28 outliers final: 14 residues processed: 115 average time/residue: 0.5346 time to fit residues: 65.0002 Evaluate side-chains 114 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117271 restraints weight = 8183.394| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.79 r_work: 0.3119 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7504 Z= 0.119 Angle : 0.510 6.292 10202 Z= 0.247 Chirality : 0.040 0.209 1224 Planarity : 0.005 0.042 1216 Dihedral : 7.809 66.825 1092 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.94 % Allowed : 16.37 % Favored : 80.69 % 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 (0.29), residues: 894 helix: 2.03 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.56 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.012 0.001 TYR B 413 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP B 492 HIS 0.003 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7502) covalent geometry : angle 0.50672 / 0.25 (10196) hydrogen bonds : bond 0.04113 / 2.77 ( 478) hydrogen bonds : angle 3.76040 / 2.66 ( 1410) link_NAG-ASN : bond 0.01100 / 0.53 ( 2) link_NAG-ASN : angle 2.42531 / 1.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.336 Fit side-chains REVERT: A 457 GLN cc_start: 0.6691 (tp-100) cc_final: 0.6355 (tp-100) REVERT: A 485 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 553 TYR cc_start: 0.9263 (m-80) cc_final: 0.8967 (m-80) REVERT: A 590 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7636 (ttmm) REVERT: A 675 PHE cc_start: 0.8780 (t80) cc_final: 0.8437 (t80) REVERT: A 721 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: B 589 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7341 (ttm170) REVERT: B 590 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7701 (ttmm) REVERT: B 721 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7844 (mpp) REVERT: B 871 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5625 (mmm160) REVERT: B 887 ASP cc_start: 0.8412 (t0) cc_final: 0.8159 (t0) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 0.5096 time to fit residues: 59.7588 Evaluate side-chains 113 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117832 restraints weight = 8243.341| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.89 r_work: 0.3124 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7504 Z= 0.110 Angle : 0.505 6.248 10202 Z= 0.247 Chirality : 0.039 0.206 1224 Planarity : 0.005 0.041 1216 Dihedral : 7.789 63.716 1092 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.69 % Allowed : 16.75 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.29), residues: 894 helix: 2.08 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.011 0.001 TYR B 486 PHE 0.011 0.001 PHE B 471 TRP 0.014 0.001 TRP B 492 HIS 0.003 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7502) covalent geometry : angle 0.50404 / 0.25 (10196) hydrogen bonds : bond 0.03965 / 2.67 ( 478) hydrogen bonds : angle 3.73924 / 2.65 ( 1410) link_NAG-ASN : bond 0.01199 / 0.57 ( 2) link_NAG-ASN : angle 1.45718 / 0.80 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.287 Fit side-chains REVERT: A 457 GLN cc_start: 0.6687 (tp-100) cc_final: 0.6374 (tp-100) REVERT: A 485 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 553 TYR cc_start: 0.9260 (m-80) cc_final: 0.8965 (m-80) REVERT: A 559 MET cc_start: 0.8493 (mmm) cc_final: 0.7706 (mmt) REVERT: A 590 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7664 (ttmm) REVERT: A 675 PHE cc_start: 0.8802 (t80) cc_final: 0.8482 (t80) REVERT: A 721 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: B 589 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: B 590 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7741 (ttmm) REVERT: B 639 LYS cc_start: 0.7579 (mmpt) cc_final: 0.6698 (mttm) REVERT: B 721 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7876 (mpp) REVERT: B 871 ARG cc_start: 0.6241 (mtm110) cc_final: 0.5579 (mmm160) REVERT: B 887 ASP cc_start: 0.8401 (t0) cc_final: 0.8140 (t0) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 0.5429 time to fit residues: 63.0485 Evaluate side-chains 113 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 625 GLN ** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117151 restraints weight = 8275.366| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.89 r_work: 0.3110 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7504 Z= 0.121 Angle : 0.512 6.273 10202 Z= 0.250 Chirality : 0.040 0.209 1224 Planarity : 0.005 0.041 1216 Dihedral : 7.654 58.533 1092 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.69 % Allowed : 17.26 % Favored : 80.05 % 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 (0.29), residues: 894 helix: 2.04 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.012 0.002 TYR B 486 PHE 0.012 0.001 PHE B 471 TRP 0.011 0.001 TRP B 492 HIS 0.004 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 7502) covalent geometry : angle 0.51166 / 0.25 (10196) hydrogen bonds : bond 0.04128 / 2.78 ( 478) hydrogen bonds : angle 3.76361 / 2.66 ( 1410) link_NAG-ASN : bond 0.00882 / 0.42 ( 2) link_NAG-ASN : angle 1.20134 / 0.67 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.49 seconds wall clock time: 40 minutes 40.83 seconds (2440.83 seconds total)