Starting phenix.real_space_refine on Thu Jul 2 07:17:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t45_41020/07_2026/8t45_41020.map" } resolution = 2.99 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 32 5.16 5 C 5020 2.51 5 N 1142 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7475 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3611 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3607 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {'NAG': 1, 'PIO': 1, 'PLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.90, per 1000 atoms: 0.25 Number of scatterers: 7475 At special positions: 0 Unit cell: (93.09, 116.63, 83.46, 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 32 16.00 P 10 15.00 O 1271 8.00 N 1142 7.00 C 5020 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 A1002 " - " ASN A 642 " " NAG B1001 " - " ASN B 642 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 405.1 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 77.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.612A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 408 " --> pdb=" O GLN A 404 " (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 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.725A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.690A pdb=" N PHE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 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 717 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 728 through 735 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: 3.734A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 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 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 873 removed outlier: 3.537A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.763A 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 403 through 431 removed outlier: 3.599A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 508 removed outlier: 3.556A pdb=" N VAL B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.622A pdb=" N VAL B 513 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 514 " --> pdb=" O PHE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 593 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 687 Processing helix chain 'B' and resid 703 through 719 removed outlier: 3.548A pdb=" N LEU B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.958A 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 800 removed outlier: 3.546A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (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 828 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 873 removed outlier: 3.570A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.682A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 3.532A pdb=" N GLY A 463 " --> pdb=" O SER A 725 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1464 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: 1.30 Time building geometry restraints manager: 0.89 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: 1079 1.31 - 1.43: 2025 1.43 - 1.56: 4479 1.56 - 1.68: 16 1.68 - 1.81: 58 Bond restraints: 7657 Sorted by residual: bond pdb=" C1A PIO B1002 " pdb=" O2C PIO B1002 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PIO A1001 " pdb=" O3C PIO A1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1B PIO B1002 " pdb=" O3C PIO B1002 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1A PIO A1001 " pdb=" O2C PIO A1001 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O4 PIO A1001 " pdb=" P4 PIO A1001 " ideal model delta sigma weight residual 1.710 1.647 0.063 2.00e-02 2.50e+03 9.95e+00 ... (remaining 7652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 10251 2.50 - 5.01: 112 5.01 - 7.51: 22 7.51 - 10.01: 5 10.01 - 12.52: 5 Bond angle restraints: 10395 Sorted by residual: angle pdb=" O1 PIO B1002 " pdb=" P1 PIO B1002 " pdb=" O13 PIO B1002 " ideal model delta sigma weight residual 97.64 110.16 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O11 PIO A1001 " pdb=" P1 PIO A1001 " pdb=" O12 PIO A1001 " ideal model delta sigma weight residual 121.09 109.09 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1 PIO A1001 " pdb=" P1 PIO A1001 " pdb=" O13 PIO A1001 " 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 B1002 " pdb=" P1 PIO B1002 " pdb=" O12 PIO B1002 " ideal model delta sigma weight residual 121.09 109.24 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C2A PIO B1002 " pdb=" C1A PIO B1002 " pdb=" O2C PIO B1002 " ideal model delta sigma weight residual 110.66 120.82 -10.16 3.00e+00 1.11e-01 1.15e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 4342 30.97 - 61.94: 165 61.94 - 92.91: 18 92.91 - 123.88: 8 123.88 - 154.85: 4 Dihedral angle restraints: 4537 sinusoidal: 1892 harmonic: 2645 Sorted by residual: dihedral pdb=" C3 PLC A1004 " pdb=" C1 PLC A1004 " pdb=" C2 PLC A1004 " pdb=" O3P PLC A1004 " ideal model delta sinusoidal sigma weight residual 67.16 -137.99 -154.85 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" O2 PLC A1004 " pdb=" C1 PLC A1004 " pdb=" C2 PLC A1004 " pdb=" O3P PLC A1004 " ideal model delta sinusoidal sigma weight residual -55.71 96.18 -151.89 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" O2 PLC A1003 " pdb=" C1 PLC A1003 " pdb=" C2 PLC A1003 " pdb=" O3P PLC A1003 " ideal model delta sinusoidal sigma weight residual 304.29 169.38 134.91 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1084 0.058 - 0.116: 149 0.116 - 0.174: 8 0.174 - 0.232: 0 0.232 - 0.289: 1 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 642 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 PIO A1001 " pdb=" C2 PIO A1001 " pdb=" C6 PIO A1001 " pdb=" O1 PIO A1001 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 783 " pdb=" N ILE A 783 " pdb=" C ILE A 783 " pdb=" CB ILE A 783 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1239 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 853 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO B 854 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 854 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 854 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 822 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 823 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 823 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 823 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 859 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 860 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 860 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 860 " 0.024 5.00e-02 4.00e+02 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 408 2.73 - 3.27: 7526 3.27 - 3.82: 12998 3.82 - 4.36: 14878 4.36 - 4.90: 26219 Nonbonded interactions: 62029 Sorted by model distance: nonbonded pdb=" OG SER A 529 " pdb=" OG SER A 799 " model vdw 2.191 3.040 nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.244 3.040 nonbonded pdb=" NH1 ARG B 646 " pdb=" O GLY B 647 " model vdw 2.246 3.120 nonbonded pdb=" NH2 ARG B 490 " pdb=" O MET B 721 " model vdw 2.259 3.120 nonbonded pdb=" OE1 GLU A 472 " pdb=" OH TYR A 486 " model vdw 2.263 3.040 ... (remaining 62024 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 402 through 687 or resid 702 through 734 or resid 753 thro \ ugh 890 or (resid 1003 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 C \ 3B or name C4' or name C4B or name C5' or name C5B or name C6' or name C6B or na \ me C7' or name C7B or name C8' or name C8B or name C9' or name C9B or name CA' o \ r name CAA 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 )) or (resid 1004 and (name CB or \ name OB or name C' or name C1 or name C1' or name C1B or name C2 or name C2' or \ name C2B or name C3 or name C3' or name C3B or name C4' or name C4B or name C5' \ or name C6' or name C7' or name C8' or name C9' or name CA' or name CB' 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 402 through 403 or (resid 404 and (name N or name CA or na \ me C or name O or name CB )) or resid 405 through 728 or (resid 729 through 730 \ and (name N or name CA or name C or name O or name CB )) or resid 731 or (resid \ 732 and (name N or name CA or name C or name O or name CB )) or resid 733 throug \ h 890 or resid 1003 through 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: 2.150 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.069 7659 Z= 0.170 Angle : 0.661 12.516 10401 Z= 0.276 Chirality : 0.039 0.289 1242 Planarity : 0.004 0.052 1236 Dihedral : 17.900 154.853 2825 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.38 % Allowed : 13.96 % Favored : 84.65 % 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: 2.32 (0.28), residues: 905 helix: 2.28 (0.20), residues: 655 sheet: None (None), residues: 0 loop : -0.49 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 646 TYR 0.014 0.001 TYR A 824 PHE 0.010 0.001 PHE B 471 TRP 0.009 0.001 TRP A 492 HIS 0.007 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 7657) covalent geometry : angle 0.65819 / 0.28 (10395) hydrogen bonds : bond 0.11372 / 7.38 ( 495) hydrogen bonds : angle 4.88966 / 3.72 ( 1464) link_NAG-ASN : bond 0.01133 / 0.54 ( 2) link_NAG-ASN : angle 2.40072 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7802 (tppt) REVERT: A 584 PHE cc_start: 0.8200 (m-80) cc_final: 0.7815 (m-80) REVERT: A 721 MET cc_start: 0.7928 (mtm) cc_final: 0.7656 (mmm) REVERT: A 827 ARG cc_start: 0.7310 (mtt180) cc_final: 0.7042 (mmm-85) REVERT: A 884 GLN cc_start: 0.6955 (tp40) cc_final: 0.6144 (tt0) REVERT: B 538 SER cc_start: 0.8420 (t) cc_final: 0.7957 (m) REVERT: B 584 PHE cc_start: 0.8245 (m-80) cc_final: 0.7890 (m-80) outliers start: 11 outliers final: 11 residues processed: 149 average time/residue: 0.5065 time to fit residues: 80.2497 Evaluate side-chains 119 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 ASN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125098 restraints weight = 8368.524| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.88 r_work: 0.3288 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7659 Z= 0.129 Angle : 0.521 6.701 10401 Z= 0.251 Chirality : 0.041 0.299 1242 Planarity : 0.005 0.049 1236 Dihedral : 14.736 148.273 1179 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.91 % Allowed : 15.85 % Favored : 79.25 % 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: 2.47 (0.29), residues: 905 helix: 2.33 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.28 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 490 TYR 0.017 0.001 TYR A 824 PHE 0.014 0.001 PHE A 679 TRP 0.011 0.001 TRP A 492 HIS 0.007 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7657) covalent geometry : angle 0.51807 / 0.25 (10395) hydrogen bonds : bond 0.03991 / 2.77 ( 495) hydrogen bonds : angle 4.14895 / 3.12 ( 1464) link_NAG-ASN : bond 0.01070 / 0.51 ( 2) link_NAG-ASN : angle 2.34517 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 551 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8000 (tppt) REVERT: A 721 MET cc_start: 0.8106 (mtm) cc_final: 0.7858 (mmm) REVERT: A 798 THR cc_start: 0.8453 (m) cc_final: 0.8199 (p) REVERT: A 827 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7421 (mmm-85) REVERT: B 538 SER cc_start: 0.8776 (t) cc_final: 0.8362 (m) REVERT: B 584 PHE cc_start: 0.8532 (m-80) cc_final: 0.8217 (m-80) REVERT: B 646 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7875 (ppt170) REVERT: B 873 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8273 (mt) outliers start: 39 outliers final: 19 residues processed: 142 average time/residue: 0.4963 time to fit residues: 75.0757 Evaluate side-chains 126 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 0.0010 chunk 78 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.0030 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN ** B 683 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 = 0.3683 r_free = 0.3683 target = 0.150059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122669 restraints weight = 8308.551| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.79 r_work: 0.3158 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7659 Z= 0.112 Angle : 0.492 5.402 10401 Z= 0.239 Chirality : 0.040 0.298 1242 Planarity : 0.005 0.048 1236 Dihedral : 13.472 143.865 1177 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.65 % Allowed : 17.36 % Favored : 78.99 % 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: 2.51 (0.28), residues: 905 helix: 2.38 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.34 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 871 TYR 0.017 0.001 TYR A 824 PHE 0.009 0.001 PHE A 471 TRP 0.010 0.001 TRP A 492 HIS 0.005 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7657) covalent geometry : angle 0.48870 / 0.24 (10395) hydrogen bonds : bond 0.03682 / 2.55 ( 495) hydrogen bonds : angle 4.00767 / 3.01 ( 1464) link_NAG-ASN : bond 0.01185 / 0.57 ( 2) link_NAG-ASN : angle 2.47407 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8491 (mt) cc_final: 0.7923 (pp) REVERT: A 512 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.5564 (tp) REVERT: A 551 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7667 (tppt) REVERT: A 721 MET cc_start: 0.7557 (mtm) cc_final: 0.7141 (mmm) REVERT: A 798 THR cc_start: 0.8047 (m) cc_final: 0.7659 (p) REVERT: B 538 SER cc_start: 0.8159 (t) cc_final: 0.7723 (m) REVERT: B 584 PHE cc_start: 0.8080 (m-80) cc_final: 0.7651 (m-80) REVERT: B 646 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7521 (ppt170) outliers start: 29 outliers final: 15 residues processed: 131 average time/residue: 0.4822 time to fit residues: 67.5232 Evaluate side-chains 120 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3673 r_free = 0.3673 target = 0.149013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121824 restraints weight = 8416.578| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7659 Z= 0.121 Angle : 0.518 8.299 10401 Z= 0.246 Chirality : 0.041 0.313 1242 Planarity : 0.005 0.049 1236 Dihedral : 12.928 141.667 1169 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.03 % Allowed : 17.11 % Favored : 78.87 % 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: 2.45 (0.29), residues: 905 helix: 2.34 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.38 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 656 TYR 0.016 0.001 TYR A 824 PHE 0.018 0.001 PHE A 679 TRP 0.011 0.001 TRP B 492 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7657) covalent geometry : angle 0.51403 / 0.25 (10395) hydrogen bonds : bond 0.03721 / 2.57 ( 495) hydrogen bonds : angle 3.99205 / 3.00 ( 1464) link_NAG-ASN : bond 0.00676 / 0.32 ( 2) link_NAG-ASN : angle 2.84037 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 512 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.5545 (tp) REVERT: A 551 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7761 (tppt) REVERT: A 721 MET cc_start: 0.7704 (mtm) cc_final: 0.7320 (mmm) REVERT: A 798 THR cc_start: 0.8135 (m) cc_final: 0.7796 (p) REVERT: A 827 ARG cc_start: 0.7420 (mtt180) cc_final: 0.7079 (mmm-85) REVERT: A 873 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 538 SER cc_start: 0.8324 (t) cc_final: 0.7887 (m) REVERT: B 584 PHE cc_start: 0.8174 (m-80) cc_final: 0.7735 (m-80) REVERT: B 602 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7852 (ttp-170) REVERT: B 646 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7650 (ppt170) REVERT: B 873 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8093 (mt) outliers start: 32 outliers final: 14 residues processed: 135 average time/residue: 0.4842 time to fit residues: 69.8017 Evaluate side-chains 122 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122148 restraints weight = 8351.820| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.76 r_work: 0.3170 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7659 Z= 0.117 Angle : 0.519 7.744 10401 Z= 0.247 Chirality : 0.041 0.314 1242 Planarity : 0.005 0.048 1236 Dihedral : 12.479 138.799 1167 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.52 % Allowed : 18.36 % Favored : 78.11 % 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: 2.44 (0.29), residues: 905 helix: 2.35 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 656 TYR 0.016 0.001 TYR A 824 PHE 0.017 0.001 PHE B 679 TRP 0.011 0.001 TRP B 492 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7657) covalent geometry : angle 0.51524 / 0.25 (10395) hydrogen bonds : bond 0.03659 / 2.53 ( 495) hydrogen bonds : angle 3.95890 / 2.97 ( 1464) link_NAG-ASN : bond 0.00779 / 0.37 ( 2) link_NAG-ASN : angle 2.63104 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7959 (pp) REVERT: A 551 LYS cc_start: 0.8431 (ptpt) cc_final: 0.7725 (tppt) REVERT: A 721 MET cc_start: 0.7616 (mtm) cc_final: 0.7212 (mmm) REVERT: A 798 THR cc_start: 0.8075 (m) cc_final: 0.7727 (p) REVERT: A 827 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7038 (mmm-85) REVERT: B 584 PHE cc_start: 0.8117 (m-80) cc_final: 0.7701 (m-80) REVERT: B 602 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7761 (ttp-170) REVERT: B 646 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7369 (ppt170) REVERT: B 656 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7501 (mtt90) REVERT: B 873 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8078 (mt) outliers start: 28 outliers final: 17 residues processed: 126 average time/residue: 0.4624 time to fit residues: 62.2164 Evaluate side-chains 121 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3677 r_free = 0.3677 target = 0.149246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122226 restraints weight = 8323.137| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.76 r_work: 0.3196 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7659 Z= 0.116 Angle : 0.509 6.796 10401 Z= 0.244 Chirality : 0.040 0.308 1242 Planarity : 0.005 0.048 1236 Dihedral : 11.903 135.541 1167 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.77 % Allowed : 17.61 % Favored : 78.62 % 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: 2.43 (0.29), residues: 905 helix: 2.37 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.55 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 656 TYR 0.015 0.001 TYR A 824 PHE 0.018 0.001 PHE A 679 TRP 0.012 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7657) covalent geometry : angle 0.50628 / 0.24 (10395) hydrogen bonds : bond 0.03644 / 2.51 ( 495) hydrogen bonds : angle 3.94179 / 2.96 ( 1464) link_NAG-ASN : bond 0.00774 / 0.37 ( 2) link_NAG-ASN : angle 2.35721 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 551 LYS cc_start: 0.8443 (ptpt) cc_final: 0.7744 (tppt) REVERT: A 656 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7839 (mtt90) REVERT: A 721 MET cc_start: 0.7625 (mtm) cc_final: 0.7224 (mmm) REVERT: A 827 ARG cc_start: 0.7399 (mtt180) cc_final: 0.7063 (mmm-85) REVERT: A 873 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8041 (mt) REVERT: B 602 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: B 646 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7801 (ppt170) outliers start: 30 outliers final: 15 residues processed: 129 average time/residue: 0.4680 time to fit residues: 64.4574 Evaluate side-chains 120 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 47 optimal weight: 0.3980 chunk 22 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3695 r_free = 0.3695 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123837 restraints weight = 8389.648| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.78 r_work: 0.3215 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7659 Z= 0.103 Angle : 0.508 8.545 10401 Z= 0.242 Chirality : 0.040 0.290 1242 Planarity : 0.005 0.048 1236 Dihedral : 11.169 132.041 1167 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.65 % Allowed : 18.62 % Favored : 77.74 % 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: 2.48 (0.29), residues: 905 helix: 2.43 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 656 TYR 0.015 0.001 TYR A 824 PHE 0.023 0.001 PHE B 679 TRP 0.016 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7657) covalent geometry : angle 0.50516 / 0.24 (10395) hydrogen bonds : bond 0.03486 / 2.41 ( 495) hydrogen bonds : angle 3.90596 / 2.94 ( 1464) link_NAG-ASN : bond 0.00711 / 0.34 ( 2) link_NAG-ASN : angle 2.19986 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8010 (pp) REVERT: A 551 LYS cc_start: 0.8439 (ptpt) cc_final: 0.7738 (tppt) REVERT: A 656 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7826 (mtt90) REVERT: A 721 MET cc_start: 0.7583 (mtm) cc_final: 0.7231 (mmm) REVERT: A 827 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7068 (mmm-85) REVERT: B 602 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7806 (ttp-170) REVERT: B 646 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7705 (ppt170) outliers start: 29 outliers final: 16 residues processed: 129 average time/residue: 0.4361 time to fit residues: 59.8732 Evaluate side-chains 118 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN B 569 ASN ** B 683 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 = 0.3680 r_free = 0.3680 target = 0.149624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122285 restraints weight = 8518.468| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.80 r_work: 0.3172 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7659 Z= 0.120 Angle : 0.525 9.234 10401 Z= 0.251 Chirality : 0.041 0.305 1242 Planarity : 0.005 0.047 1236 Dihedral : 10.942 127.705 1167 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 18.99 % Favored : 77.86 % 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: 2.36 (0.29), residues: 905 helix: 2.35 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.70 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 514 TYR 0.015 0.001 TYR A 824 PHE 0.019 0.001 PHE A 679 TRP 0.019 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7657) covalent geometry : angle 0.52238 / 0.25 (10395) hydrogen bonds : bond 0.03657 / 2.52 ( 495) hydrogen bonds : angle 3.95303 / 2.97 ( 1464) link_NAG-ASN : bond 0.00750 / 0.36 ( 2) link_NAG-ASN : angle 2.29430 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 551 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7757 (tppt) REVERT: A 625 GLN cc_start: 0.7759 (mp10) cc_final: 0.6955 (mt0) REVERT: A 721 MET cc_start: 0.7631 (mtm) cc_final: 0.7253 (mmm) REVERT: A 827 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7079 (mmm-85) REVERT: A 873 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (mt) REVERT: B 602 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7737 (ttp-170) REVERT: B 646 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7873 (ppt170) REVERT: B 873 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8096 (mt) outliers start: 25 outliers final: 15 residues processed: 121 average time/residue: 0.4323 time to fit residues: 55.9454 Evaluate side-chains 116 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3673 r_free = 0.3673 target = 0.149053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122233 restraints weight = 8380.911| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.76 r_work: 0.3201 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.003 0.033 7659 Z= 0.119 Angle : 0.532 8.859 10401 Z= 0.253 Chirality : 0.041 0.298 1242 Planarity : 0.005 0.047 1236 Dihedral : 10.740 122.299 1167 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.52 % Allowed : 20.25 % Favored : 77.23 % 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: 2.33 (0.28), residues: 905 helix: 2.34 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 656 TYR 0.015 0.001 TYR A 824 PHE 0.024 0.001 PHE B 679 TRP 0.017 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7657) covalent geometry : angle 0.52904 / 0.25 (10395) hydrogen bonds : bond 0.03645 / 2.52 ( 495) hydrogen bonds : angle 3.96183 / 2.97 ( 1464) link_NAG-ASN : bond 0.00720 / 0.34 ( 2) link_NAG-ASN : angle 2.20601 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8006 (pp) REVERT: A 551 LYS cc_start: 0.8469 (ptpt) cc_final: 0.7737 (tppt) REVERT: A 625 GLN cc_start: 0.7743 (mp10) cc_final: 0.6949 (mt0) REVERT: A 721 MET cc_start: 0.7637 (mtm) cc_final: 0.7243 (mmm) REVERT: A 827 ARG cc_start: 0.7436 (mtt180) cc_final: 0.7088 (mmm-85) REVERT: A 871 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7745 (mmm-85) REVERT: A 873 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 602 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7736 (ttp-170) REVERT: B 646 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7802 (ppt170) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.4250 time to fit residues: 52.7838 Evaluate side-chains 117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3686 r_free = 0.3686 target = 0.150252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123263 restraints weight = 8338.766| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.77 r_work: 0.3232 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7659 Z= 0.112 Angle : 0.522 8.874 10401 Z= 0.250 Chirality : 0.040 0.295 1242 Planarity : 0.005 0.047 1236 Dihedral : 10.528 115.348 1167 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.02 % Allowed : 19.62 % Favored : 77.36 % 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: 2.30 (0.29), residues: 905 helix: 2.32 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.015 0.001 TYR A 824 PHE 0.025 0.001 PHE A 679 TRP 0.023 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7657) covalent geometry : angle 0.51961 / 0.25 (10395) hydrogen bonds : bond 0.03567 / 2.47 ( 495) hydrogen bonds : angle 3.95266 / 2.96 ( 1464) link_NAG-ASN : bond 0.00693 / 0.33 ( 2) link_NAG-ASN : angle 2.14690 / 1.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 551 LYS cc_start: 0.8487 (ptpt) cc_final: 0.7788 (tppt) REVERT: A 625 GLN cc_start: 0.7791 (mp10) cc_final: 0.7026 (mt0) REVERT: A 650 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7116 (pp) REVERT: A 656 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7843 (mtt90) REVERT: A 721 MET cc_start: 0.7711 (mtm) cc_final: 0.7323 (mmm) REVERT: A 827 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7144 (mmm-85) REVERT: A 871 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: B 602 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7835 (ttp-170) REVERT: B 646 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7667 (ppt170) REVERT: B 684 ILE cc_start: 0.6420 (pp) cc_final: 0.6004 (mt) REVERT: B 721 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: B 871 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7715 (mmm-85) outliers start: 24 outliers final: 15 residues processed: 118 average time/residue: 0.4588 time to fit residues: 57.7845 Evaluate side-chains 117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** B 683 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 = 0.3677 r_free = 0.3677 target = 0.149307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122137 restraints weight = 8363.357| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.78 r_work: 0.3219 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7659 Z= 0.123 Angle : 0.536 8.688 10401 Z= 0.257 Chirality : 0.041 0.303 1242 Planarity : 0.005 0.047 1236 Dihedral : 10.457 110.229 1167 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.02 % Allowed : 20.25 % Favored : 76.73 % 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: 2.22 (0.28), residues: 905 helix: 2.25 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.015 0.001 TYR A 824 PHE 0.023 0.001 PHE B 679 TRP 0.025 0.001 TRP B 492 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 7657) covalent geometry : angle 0.53328 / 0.26 (10395) hydrogen bonds : bond 0.03681 / 2.55 ( 495) hydrogen bonds : angle 3.98458 / 2.98 ( 1464) link_NAG-ASN : bond 0.00726 / 0.35 ( 2) link_NAG-ASN : angle 2.19142 / 1.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.68 seconds wall clock time: 41 minutes 57.14 seconds (2517.14 seconds total)