Starting phenix.real_space_refine on Thu Sep 10 21:48:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wr7_32717/09_2026/7wr7_32717.cif" } resolution = 3.1 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 34 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2509 2.51 5 N 681 2.21 5 O 776 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3995 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain: "B" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'GBS': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GBS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.28 Number of scatterers: 3995 At special positions: 0 Unit cell: (64.852, 80.542, 95.186, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 776 8.00 N 681 7.00 C 2509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 534 " " NAG A 802 " - " ASN A 630 " " NAG A 803 " - " ASN A 682 " " NAG A 804 " - " ASN A 706 " " NAG A 805 " - " ASN A 725 " " NAG B1101 " - " ASN B 848 " " NAG B1102 " - " ASN B 887 " " NAG B1103 " - " ASN B 909 " " NAG B1104 " - " ASN B 949 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 106.3 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 7.9% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.071A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 538 removed outlier: 3.744A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 572 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 632 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 566 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY A 634 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 564 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.757A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 594 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA4, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.899A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 740 through 741 removed outlier: 3.705A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.856A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 914 " --> pdb=" O GLN B 929 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASN B 909 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN B 978 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 975 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 977 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 820 through 821 removed outlier: 5.813A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 802 " --> pdb=" O CYS B 810 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 198 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: 0.35 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1015 1.33 - 1.45: 823 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4092 Sorted by residual: bond pdb=" C18 GBS B1105 " pdb=" N3 GBS B1105 " ideal model delta sigma weight residual 1.387 1.333 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" N GLN B 968 " pdb=" CA GLN B 968 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.52e+00 bond pdb=" O GBS B1105 " pdb=" C6 GBS B1105 " ideal model delta sigma weight residual 1.260 1.210 0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" N SER B 971 " pdb=" CA SER B 971 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N GLY B 973 " pdb=" CA GLY B 973 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.37e-02 5.33e+03 5.83e+00 ... (remaining 4087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 5343 1.40 - 2.81: 185 2.81 - 4.21: 31 4.21 - 5.62: 5 5.62 - 7.02: 5 Bond angle restraints: 5569 Sorted by residual: angle pdb=" N ASP B 970 " pdb=" CA ASP B 970 " pdb=" C ASP B 970 " ideal model delta sigma weight residual 114.56 108.41 6.15 1.27e+00 6.20e-01 2.35e+01 angle pdb=" N PRO B 974 " pdb=" CA PRO B 974 " pdb=" CB PRO B 974 " ideal model delta sigma weight residual 103.25 98.83 4.42 1.05e+00 9.07e-01 1.77e+01 angle pdb=" CA GLN B 968 " pdb=" C GLN B 968 " pdb=" O GLN B 968 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.31e+00 angle pdb=" N GLY B 972 " pdb=" CA GLY B 972 " pdb=" C GLY B 972 " ideal model delta sigma weight residual 115.32 111.24 4.08 1.38e+00 5.25e-01 8.75e+00 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 109.81 115.70 -5.89 2.21e+00 2.05e-01 7.10e+00 ... (remaining 5564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 2232 16.22 - 32.45: 97 32.45 - 48.67: 22 48.67 - 64.89: 5 64.89 - 81.12: 1 Dihedral angle restraints: 2357 sinusoidal: 945 harmonic: 1412 Sorted by residual: dihedral pdb=" CA PRO A 543 " pdb=" C PRO A 543 " pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " pdb=" SG CYS B 896 " pdb=" CB CYS B 896 " ideal model delta sinusoidal sigma weight residual -86.00 -113.70 27.70 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 404 0.033 - 0.067: 140 0.067 - 0.100: 55 0.100 - 0.134: 28 0.134 - 0.167: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL B 988 " pdb=" N VAL B 988 " pdb=" C VAL B 988 " pdb=" CB VAL B 988 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CB VAL A 691 " pdb=" CA VAL A 691 " pdb=" CG1 VAL A 691 " pdb=" CG2 VAL A 691 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 625 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 GBS B1105 " 0.013 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" C2 GBS B1105 " -0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " 0.055 2.00e-02 2.50e+03 pdb=" N3 GBS B1105 " -0.034 2.00e-02 2.50e+03 pdb=" N4 GBS B1105 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GBS B1105 " -0.026 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" C1 GBS B1105 " 0.009 2.00e-02 2.50e+03 pdb=" C2 GBS B1105 " 0.028 2.00e-02 2.50e+03 pdb=" C3 GBS B1105 " 0.008 2.00e-02 2.50e+03 pdb=" C4 GBS B1105 " -0.026 2.00e-02 2.50e+03 pdb=" C5 GBS B1105 " -0.031 2.00e-02 2.50e+03 pdb=" C6 GBS B1105 " 0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 533 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1243 2.83 - 3.35: 3694 3.35 - 3.86: 6398 3.86 - 4.38: 7329 4.38 - 4.90: 12603 Nonbonded interactions: 31267 Sorted by model distance: nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.309 3.120 nonbonded pdb=" NH2 ARG B 908 " pdb=" O GLN B 978 " model vdw 2.350 3.120 nonbonded pdb=" O GLY B 811 " pdb=" O GLY B 972 " model vdw 2.357 3.040 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 3.120 nonbonded pdb=" O CYS B 826 " pdb=" NH1 ARG B 830 " model vdw 2.367 3.120 ... (remaining 31262 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.145 4110 Z= 0.304 Angle : 0.610 7.023 5612 Z= 0.331 Chirality : 0.044 0.167 628 Planarity : 0.003 0.039 724 Dihedral : 9.664 81.116 1429 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.29 % Allowed : 6.59 % Favored : 90.12 % 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: -4.53 (0.30), residues: 492 helix: -2.64 (0.51), residues: 36 sheet: -2.64 (0.42), residues: 105 loop : -3.42 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 807 TYR 0.004 0.001 TYR A 546 PHE 0.005 0.001 PHE A 627 TRP 0.003 0.000 TRP A 699 HIS 0.002 0.000 HIS B 825 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.20 ( 4092) covalent geometry : angle 0.60678 / 0.33 ( 5569) SS BOND : bond 0.00114 / 0.06 ( 8) SS BOND : angle 0.47116 / 0.27 ( 16) hydrogen bonds : bond 0.24605 / 15.37 ( 77) hydrogen bonds : angle 10.72767 / 7.43 ( 198) Misc. bond : bond 0.14536 / 7.65 ( 1) link_NAG-ASN : bond 0.00213 / 0.12 ( 9) link_NAG-ASN : angle 1.09755 / 0.71 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.7770 (mtm110) REVERT: A 707 TRP cc_start: 0.8525 (t-100) cc_final: 0.7934 (t-100) REVERT: B 959 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-10) outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 0.0902 time to fit residues: 12.7965 Evaluate side-chains 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.7262 > 50:) chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN A 713 ASN A 717 GLN B 844 HIS B 921 GLN B 938 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.178921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127836 restraints weight = 5304.722| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.77 r_work: 0.3601 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4110 Z= 0.154 Angle : 0.604 9.180 5612 Z= 0.304 Chirality : 0.047 0.254 628 Planarity : 0.004 0.045 724 Dihedral : 5.370 53.336 535 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.82 % Allowed : 13.18 % Favored : 84.00 % 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: -3.84 (0.34), residues: 492 helix: -1.88 (0.70), residues: 38 sheet: -2.29 (0.39), residues: 120 loop : -2.91 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 807 TYR 0.007 0.001 TYR B 803 PHE 0.011 0.001 PHE A 693 TRP 0.010 0.001 TRP B1013 HIS 0.007 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4092) covalent geometry : angle 0.59739 / 0.30 ( 5569) SS BOND : bond 0.00509 / 0.32 ( 8) SS BOND : angle 1.02905 / 0.55 ( 16) hydrogen bonds : bond 0.04250 / 2.84 ( 77) hydrogen bonds : angle 6.68225 / 4.63 ( 198) Misc. bond : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : bond 0.00290 / 0.16 ( 9) link_NAG-ASN : angle 1.22699 / 0.82 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 TRP cc_start: 0.8675 (t-100) cc_final: 0.7980 (t-100) REVERT: A 728 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7939 (pttp) REVERT: A 751 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 766 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7325 (mm-40) REVERT: B 803 TYR cc_start: 0.8455 (m-80) cc_final: 0.7986 (m-80) REVERT: B 859 ILE cc_start: 0.8343 (mm) cc_final: 0.7967 (mm) REVERT: B 954 MET cc_start: 0.7483 (mtt) cc_final: 0.7237 (mtm) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.0777 time to fit residues: 7.7400 Evaluate side-chains 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 938 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127147 restraints weight = 5311.221| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.61 r_work: 0.3566 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4110 Z= 0.177 Angle : 0.605 9.298 5612 Z= 0.304 Chirality : 0.046 0.242 628 Planarity : 0.005 0.056 724 Dihedral : 5.073 54.855 532 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 3.29 % Allowed : 12.47 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.35), residues: 492 helix: -1.28 (0.78), residues: 38 sheet: -2.02 (0.41), residues: 115 loop : -2.81 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 692 TYR 0.007 0.001 TYR B 920 PHE 0.010 0.001 PHE A 731 TRP 0.007 0.001 TRP A 531 HIS 0.006 0.001 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 4092) covalent geometry : angle 0.60077 / 0.30 ( 5569) SS BOND : bond 0.00371 / 0.22 ( 8) SS BOND : angle 0.80183 / 0.43 ( 16) hydrogen bonds : bond 0.03580 / 2.42 ( 77) hydrogen bonds : angle 6.17028 / 4.22 ( 198) Misc. bond : bond 0.00041 / 0.02 ( 1) link_NAG-ASN : bond 0.00227 / 0.12 ( 9) link_NAG-ASN : angle 1.16440 / 0.74 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 679 ARG cc_start: 0.8726 (ptp-170) cc_final: 0.8231 (mtm110) REVERT: A 717 GLN cc_start: 0.8816 (pp30) cc_final: 0.8592 (pp30) REVERT: A 728 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7635 (pttp) REVERT: A 751 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8099 (pp) REVERT: A 764 ARG cc_start: 0.7027 (mpt180) cc_final: 0.6792 (mpt180) REVERT: A 766 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7326 (mm-40) REVERT: B 803 TYR cc_start: 0.8492 (m-80) cc_final: 0.7717 (m-80) REVERT: B 859 ILE cc_start: 0.8355 (mm) cc_final: 0.7998 (mm) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.0779 time to fit residues: 7.8829 Evaluate side-chains 80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 0.0030 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 ASN A 660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.177156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127915 restraints weight = 5197.258| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.62 r_work: 0.3570 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4110 Z= 0.135 Angle : 0.583 9.358 5612 Z= 0.294 Chirality : 0.046 0.250 628 Planarity : 0.004 0.046 724 Dihedral : 5.016 55.381 532 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 2.35 % Allowed : 16.24 % Favored : 81.41 % 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: -3.28 (0.36), residues: 492 helix: -1.10 (0.81), residues: 38 sheet: -1.65 (0.43), residues: 116 loop : -2.68 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 807 TYR 0.007 0.001 TYR B 920 PHE 0.010 0.001 PHE A 542 TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4092) covalent geometry : angle 0.57936 / 0.29 ( 5569) SS BOND : bond 0.00314 / 0.19 ( 8) SS BOND : angle 0.75645 / 0.41 ( 16) hydrogen bonds : bond 0.02990 / 2.07 ( 77) hydrogen bonds : angle 5.69939 / 3.89 ( 198) Misc. bond : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : bond 0.00234 / 0.12 ( 9) link_NAG-ASN : angle 1.05457 / 0.64 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 679 ARG cc_start: 0.8693 (ptp-170) cc_final: 0.8433 (ptp-170) REVERT: A 692 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6977 (ttm-80) REVERT: A 717 GLN cc_start: 0.8916 (pp30) cc_final: 0.8651 (pp30) REVERT: A 751 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (pp) REVERT: B 803 TYR cc_start: 0.8503 (m-80) cc_final: 0.7540 (m-80) REVERT: B 859 ILE cc_start: 0.8330 (mm) cc_final: 0.7972 (mm) REVERT: B 993 TYR cc_start: 0.7966 (t80) cc_final: 0.7753 (t80) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.0836 time to fit residues: 7.7604 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 41 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN ** A 660 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.178945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.128716 restraints weight = 5226.914| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.67 r_work: 0.3600 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4110 Z= 0.105 Angle : 0.563 9.421 5612 Z= 0.284 Chirality : 0.046 0.245 628 Planarity : 0.005 0.061 724 Dihedral : 4.660 53.610 531 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.06 % Allowed : 15.06 % Favored : 81.88 % 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: -2.98 (0.36), residues: 492 helix: -0.92 (0.84), residues: 38 sheet: -1.30 (0.45), residues: 116 loop : -2.53 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 764 TYR 0.008 0.001 TYR B 920 PHE 0.010 0.001 PHE A 542 TRP 0.005 0.001 TRP B 798 HIS 0.003 0.000 HIS A 769 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 4092) covalent geometry : angle 0.56012 / 0.28 ( 5569) SS BOND : bond 0.00241 / 0.15 ( 8) SS BOND : angle 0.66031 / 0.37 ( 16) hydrogen bonds : bond 0.02705 / 1.90 ( 77) hydrogen bonds : angle 5.19619 / 3.50 ( 198) Misc. bond : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : bond 0.00272 / 0.14 ( 9) link_NAG-ASN : angle 0.91008 / 0.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: A 679 ARG cc_start: 0.8683 (ptp-170) cc_final: 0.8414 (ptp-170) REVERT: A 717 GLN cc_start: 0.8928 (pp30) cc_final: 0.8640 (pp30) REVERT: B 803 TYR cc_start: 0.8472 (m-80) cc_final: 0.7507 (m-80) REVERT: B 859 ILE cc_start: 0.8241 (mm) cc_final: 0.7917 (mm) REVERT: B 993 TYR cc_start: 0.7878 (t80) cc_final: 0.7653 (t80) outliers start: 13 outliers final: 5 residues processed: 70 average time/residue: 0.0720 time to fit residues: 6.3718 Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN ** A 660 ASN ** 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 = 0.4303 r_free = 0.4303 target = 0.168402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119816 restraints weight = 5151.614| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.41 r_work: 0.3588 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4110 Z= 0.146 Angle : 0.581 9.349 5612 Z= 0.295 Chirality : 0.047 0.241 628 Planarity : 0.005 0.046 724 Dihedral : 4.882 55.334 531 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.35 % Allowed : 16.24 % Favored : 81.41 % 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: -2.90 (0.36), residues: 492 helix: -0.82 (0.85), residues: 38 sheet: -1.29 (0.45), residues: 116 loop : -2.46 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 807 TYR 0.007 0.001 TYR B 920 PHE 0.009 0.001 PHE A 542 TRP 0.005 0.001 TRP B 798 HIS 0.003 0.001 HIS B 825 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4092) covalent geometry : angle 0.57799 / 0.29 ( 5569) SS BOND : bond 0.00311 / 0.19 ( 8) SS BOND : angle 0.76619 / 0.42 ( 16) hydrogen bonds : bond 0.02775 / 1.94 ( 77) hydrogen bonds : angle 5.25952 / 3.51 ( 198) Misc. bond : bond 0.00050 / 0.03 ( 1) link_NAG-ASN : bond 0.00195 / 0.10 ( 9) link_NAG-ASN : angle 0.98310 / 0.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: A 679 ARG cc_start: 0.8679 (ptp-170) cc_final: 0.8406 (ptp-170) REVERT: A 717 GLN cc_start: 0.8930 (pp30) cc_final: 0.8619 (pp30) REVERT: B 803 TYR cc_start: 0.8548 (m-80) cc_final: 0.7529 (m-80) REVERT: B 859 ILE cc_start: 0.8290 (mm) cc_final: 0.7948 (mm) REVERT: B 879 MET cc_start: 0.8009 (mtp) cc_final: 0.7702 (mmm) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.0659 time to fit residues: 5.2841 Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN ** A 660 ASN ** 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 = 0.4291 r_free = 0.4291 target = 0.168238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.117697 restraints weight = 5200.609| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.57 r_work: 0.3569 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4110 Z= 0.135 Angle : 0.583 9.373 5612 Z= 0.297 Chirality : 0.047 0.240 628 Planarity : 0.005 0.066 724 Dihedral : 4.861 54.087 531 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.35 % Allowed : 16.71 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.37), residues: 492 helix: -0.77 (0.85), residues: 38 sheet: -1.30 (0.45), residues: 116 loop : -2.40 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 692 TYR 0.009 0.001 TYR B 920 PHE 0.011 0.001 PHE A 681 TRP 0.005 0.001 TRP B 798 HIS 0.002 0.001 HIS A 769 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4092) covalent geometry : angle 0.58007 / 0.30 ( 5569) SS BOND : bond 0.00288 / 0.18 ( 8) SS BOND : angle 0.73435 / 0.41 ( 16) hydrogen bonds : bond 0.02653 / 1.87 ( 77) hydrogen bonds : angle 5.19076 / 3.47 ( 198) Misc. bond : bond 0.00043 / 0.02 ( 1) link_NAG-ASN : bond 0.00200 / 0.10 ( 9) link_NAG-ASN : angle 0.95866 / 0.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: A 717 GLN cc_start: 0.8935 (pp30) cc_final: 0.8635 (pp30) REVERT: B 803 TYR cc_start: 0.8591 (m-80) cc_final: 0.7543 (m-80) REVERT: B 859 ILE cc_start: 0.8279 (mm) cc_final: 0.7942 (mm) REVERT: B 879 MET cc_start: 0.7940 (mtp) cc_final: 0.7639 (mmm) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0673 time to fit residues: 5.4271 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.158623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110870 restraints weight = 5290.471| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.38 r_work: 0.3513 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4110 Z= 0.148 Angle : 0.592 9.350 5612 Z= 0.302 Chirality : 0.046 0.239 628 Planarity : 0.005 0.066 724 Dihedral : 4.978 55.525 531 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.35 % Allowed : 16.47 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.37), residues: 492 helix: -0.72 (0.85), residues: 38 sheet: -1.38 (0.44), residues: 116 loop : -2.36 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 807 TYR 0.009 0.001 TYR B 920 PHE 0.037 0.002 PHE A 681 TRP 0.010 0.001 TRP A 707 HIS 0.004 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4092) covalent geometry : angle 0.58935 / 0.30 ( 5569) SS BOND : bond 0.00305 / 0.19 ( 8) SS BOND : angle 0.77241 / 0.43 ( 16) hydrogen bonds : bond 0.02696 / 1.83 ( 77) hydrogen bonds : angle 5.22349 / 3.47 ( 198) Misc. bond : bond 0.00053 / 0.03 ( 1) link_NAG-ASN : bond 0.00194 / 0.10 ( 9) link_NAG-ASN : angle 0.94669 / 0.55 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7251 (mm-40) REVERT: B 803 TYR cc_start: 0.8608 (m-80) cc_final: 0.7598 (m-80) REVERT: B 859 ILE cc_start: 0.8322 (mm) cc_final: 0.7978 (mm) REVERT: B 879 MET cc_start: 0.7958 (mtp) cc_final: 0.7653 (mmm) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.0641 time to fit residues: 5.0822 Evaluate side-chains 61 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 41 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111128 restraints weight = 5355.743| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.43 r_work: 0.3526 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4110 Z= 0.131 Angle : 0.607 9.361 5612 Z= 0.311 Chirality : 0.046 0.237 628 Planarity : 0.005 0.067 724 Dihedral : 4.973 55.701 531 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.82 % Allowed : 15.76 % Favored : 81.41 % 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: -2.80 (0.37), residues: 492 helix: -0.66 (0.85), residues: 38 sheet: -1.32 (0.45), residues: 116 loop : -2.35 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 692 TYR 0.008 0.001 TYR B 920 PHE 0.008 0.001 PHE A 537 TRP 0.009 0.001 TRP A 707 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4092) covalent geometry : angle 0.60376 / 0.31 ( 5569) SS BOND : bond 0.00276 / 0.17 ( 8) SS BOND : angle 0.69068 / 0.39 ( 16) hydrogen bonds : bond 0.02588 / 1.79 ( 77) hydrogen bonds : angle 5.14366 / 3.42 ( 198) Misc. bond : bond 0.00041 / 0.02 ( 1) link_NAG-ASN : bond 0.00249 / 0.13 ( 9) link_NAG-ASN : angle 1.00164 / 0.60 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8654 (ptp-170) cc_final: 0.8378 (ptp-170) REVERT: A 766 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7247 (mm-40) REVERT: B 803 TYR cc_start: 0.8615 (m-80) cc_final: 0.7580 (m-80) REVERT: B 859 ILE cc_start: 0.8305 (mm) cc_final: 0.7966 (mm) REVERT: B 879 MET cc_start: 0.7961 (mtp) cc_final: 0.7678 (mmm) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.0624 time to fit residues: 5.2260 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 GLN ** A 660 ASN ** 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 = 0.4058 r_free = 0.4058 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103247 restraints weight = 5309.029| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.61 r_work: 0.3306 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4110 Z= 0.150 Angle : 0.621 9.307 5612 Z= 0.320 Chirality : 0.046 0.232 628 Planarity : 0.006 0.068 724 Dihedral : 5.106 56.506 531 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.12 % Allowed : 17.65 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.36), residues: 492 helix: -0.58 (0.85), residues: 38 sheet: -1.45 (0.44), residues: 116 loop : -2.37 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 807 TYR 0.008 0.001 TYR B 920 PHE 0.038 0.002 PHE A 681 TRP 0.009 0.001 TRP A 699 HIS 0.004 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4092) covalent geometry : angle 0.61618 / 0.32 ( 5569) SS BOND : bond 0.00287 / 0.18 ( 8) SS BOND : angle 0.78181 / 0.44 ( 16) hydrogen bonds : bond 0.02672 / 1.85 ( 77) hydrogen bonds : angle 5.24137 / 3.47 ( 198) Misc. bond : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : bond 0.00240 / 0.13 ( 9) link_NAG-ASN : angle 1.23284 / 0.69 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7786 (tp) cc_final: 0.7238 (pp) REVERT: A 679 ARG cc_start: 0.8587 (ptp-170) cc_final: 0.7318 (ptp-170) REVERT: A 717 GLN cc_start: 0.9017 (pp30) cc_final: 0.8754 (pp30) REVERT: B 803 TYR cc_start: 0.8671 (m-80) cc_final: 0.7596 (m-80) REVERT: B 859 ILE cc_start: 0.8348 (mm) cc_final: 0.8008 (mm) REVERT: B 879 MET cc_start: 0.8054 (mtp) cc_final: 0.7773 (mmm) REVERT: B 959 TYR cc_start: 0.8140 (m-10) cc_final: 0.7521 (m-10) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.0631 time to fit residues: 4.9891 Evaluate side-chains 58 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.150715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107198 restraints weight = 5259.198| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.30 r_work: 0.3341 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4110 Z= 0.134 Angle : 0.627 9.340 5612 Z= 0.322 Chirality : 0.047 0.233 628 Planarity : 0.005 0.068 724 Dihedral : 5.054 56.471 531 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 1.65 % Allowed : 18.59 % Favored : 79.76 % 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: -2.81 (0.36), residues: 492 helix: -0.62 (0.84), residues: 38 sheet: -1.40 (0.44), residues: 116 loop : -2.34 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 692 TYR 0.008 0.001 TYR B 920 PHE 0.033 0.002 PHE A 681 TRP 0.026 0.002 TRP A 699 HIS 0.003 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4092) covalent geometry : angle 0.62460 / 0.32 ( 5569) SS BOND : bond 0.00299 / 0.18 ( 8) SS BOND : angle 0.70054 / 0.39 ( 16) hydrogen bonds : bond 0.02531 / 1.76 ( 77) hydrogen bonds : angle 5.17985 / 3.43 ( 198) Misc. bond : bond 0.00040 / 0.02 ( 1) link_NAG-ASN : bond 0.00248 / 0.12 ( 9) link_NAG-ASN : angle 0.96483 / 0.55 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.99 seconds wall clock time: 21 minutes 51.40 seconds (1311.40 seconds total)