Starting phenix.real_space_refine on Tue Aug 4 20:18:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q69_72260/08_2026/9q69_72260.map" } resolution = 3.35 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= -0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4031 2.51 5 N 1087 2.21 5 O 1267 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6429 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 811 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 901 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1208 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Time building chain proxies: 1.41, per 1000 atoms: 0.22 Number of scatterers: 6429 At special positions: 0 Unit cell: (96.93, 101.956, 123.496, 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 44 16.00 O 1267 8.00 N 1087 7.00 C 4031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 754 " - pdb=" SG CYS G 766 " distance=2.03 Simple disulfide: pdb=" SG CYS G 772 " - pdb=" SG CYS G 788 " distance=2.03 Simple disulfide: pdb=" SG CYS G 781 " - pdb=" SG CYS G 799 " distance=2.03 Simple disulfide: pdb=" SG CYS G 801 " - pdb=" SG CYS G 813 " distance=2.03 Simple disulfide: pdb=" SG CYS G 819 " - pdb=" SG CYS G 830 " distance=2.03 Simple disulfide: pdb=" SG CYS G 824 " - pdb=" SG CYS G 839 " distance=2.03 Simple disulfide: pdb=" SG CYS G 841 " - pdb=" SG CYS G 853 " distance=2.03 Simple disulfide: pdb=" SG CYS G 859 " - pdb=" SG CYS G 872 " distance=2.03 Simple disulfide: pdb=" SG CYS G 866 " - pdb=" SG CYS G 882 " distance=2.03 Simple disulfide: pdb=" SG CYS G 884 " - pdb=" SG CYS G 896 " 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=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 338.0 milliseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 26 sheets defined 2.9% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.891A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR A 87 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.577A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 removed outlier: 3.721A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.594A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.594A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.542A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.526A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.526A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.621A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.677A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET C 82 " --> pdb=" O LEU C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.785A pdb=" N ASP C 58 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.785A pdb=" N ASP C 58 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.737A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 79 " --> pdb=" O SER C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.522A pdb=" N THR D 105 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS D 39 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.707A pdb=" N VAL D 97 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'E' and resid 46 through 47 removed outlier: 3.704A pdb=" N VAL E 102 " --> pdb=" O HIS E 94 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR E 96 " --> pdb=" O MET E 100E" (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET E 100E" --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.468A pdb=" N ALA F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.468A pdb=" N ALA F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 24 removed outlier: 3.720A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 786 through 789 removed outlier: 3.538A pdb=" N GLU G 800 " --> pdb=" O MET G 787 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA G 789 " --> pdb=" O LYS G 798 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 805 through 807 Processing sheet with id=AC5, first strand: chain 'G' and resid 828 through 833 Processing sheet with id=AC6, first strand: chain 'G' and resid 845 through 847 removed outlier: 3.610A pdb=" N LYS G 846 " --> pdb=" O ILE G 854 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 854 " --> pdb=" O LYS G 846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 870 through 873 Processing sheet with id=AC8, first strand: chain 'G' and resid 889 through 891 221 hydrogen bonds defined for protein. 552 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: 1.17 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2070 1.34 - 1.46: 1617 1.46 - 1.59: 2832 1.59 - 1.71: 0 1.71 - 1.83: 55 Bond restraints: 6574 Sorted by residual: bond pdb=" C LEU D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.19e-02 7.06e+03 5.90e+00 bond pdb=" CB ASP C 72 " pdb=" CG ASP C 72 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.21e+00 bond pdb=" CA ASP C 72 " pdb=" CB ASP C 72 " ideal model delta sigma weight residual 1.532 1.558 -0.025 1.56e-02 4.11e+03 2.67e+00 bond pdb=" CB ASP C 53 " pdb=" CG ASP C 53 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.62e+00 bond pdb=" CG1 ILE D 48 " pdb=" CD1 ILE D 48 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 ... (remaining 6569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 8743 2.40 - 4.79: 155 4.79 - 7.19: 15 7.19 - 9.58: 5 9.58 - 11.98: 1 Bond angle restraints: 8919 Sorted by residual: angle pdb=" C ARG C 71 " pdb=" N ASP C 72 " pdb=" CA ASP C 72 " ideal model delta sigma weight residual 123.05 130.32 -7.27 1.57e+00 4.06e-01 2.15e+01 angle pdb=" C ALA D 27 " pdb=" N LEU D 28 " pdb=" CA LEU D 28 " ideal model delta sigma weight residual 120.06 125.32 -5.26 1.19e+00 7.06e-01 1.95e+01 angle pdb=" C ALA C 52C" pdb=" N ASP C 53 " pdb=" CA ASP C 53 " ideal model delta sigma weight residual 125.66 133.52 -7.86 1.85e+00 2.92e-01 1.81e+01 angle pdb=" C GLU C 1 " pdb=" N VAL C 2 " pdb=" CA VAL C 2 " ideal model delta sigma weight residual 121.97 129.06 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" CA ASP C 72 " pdb=" CB ASP C 72 " pdb=" CG ASP C 72 " ideal model delta sigma weight residual 112.60 116.13 -3.53 1.00e+00 1.00e+00 1.24e+01 ... (remaining 8914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3582 17.94 - 35.87: 281 35.87 - 53.80: 45 53.80 - 71.74: 16 71.74 - 89.67: 5 Dihedral angle restraints: 3929 sinusoidal: 1542 harmonic: 2387 Sorted by residual: dihedral pdb=" CB CYS G 884 " pdb=" SG CYS G 884 " pdb=" SG CYS G 896 " pdb=" CB CYS G 896 " ideal model delta sinusoidal sigma weight residual -86.00 -174.70 88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 19.82 73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS G 824 " pdb=" SG CYS G 824 " pdb=" SG CYS G 839 " pdb=" CB CYS G 839 " ideal model delta sinusoidal sigma weight residual 93.00 152.58 -59.58 1 1.00e+01 1.00e-02 4.74e+01 ... (remaining 3926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 756 0.056 - 0.112: 181 0.112 - 0.168: 31 0.168 - 0.223: 1 0.223 - 0.279: 2 Chirality restraints: 971 Sorted by residual: chirality pdb=" CB THR F 42 " pdb=" CA THR F 42 " pdb=" OG1 THR F 42 " pdb=" CG2 THR F 42 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB THR C 87 " pdb=" CA THR C 87 " pdb=" OG1 THR C 87 " pdb=" CG2 THR C 87 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ASP C 72 " pdb=" N ASP C 72 " pdb=" C ASP C 72 " pdb=" CB ASP C 72 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 968 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 52 " 0.023 2.00e-02 2.50e+03 1.90e-02 9.04e+00 pdb=" CG TRP A 52 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 52 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 52 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 52 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 52 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 52 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 52 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 28 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO D 29 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 83 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO E 84 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 84 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 84 " -0.034 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 3915 3.06 - 3.52: 6354 3.52 - 3.98: 10450 3.98 - 4.44: 12118 4.44 - 4.90: 19721 Nonbonded interactions: 52558 Sorted by model distance: nonbonded pdb=" N HIS E 100 " pdb=" O HIS E 100 " model vdw 2.595 2.496 nonbonded pdb=" N GLU C 1 " pdb=" N VAL C 2 " model vdw 2.613 2.560 nonbonded pdb=" N SER D 1 " pdb=" N TYR D 2 " model vdw 2.613 2.560 nonbonded pdb=" O ARG C 71 " pdb=" OD1 ASP C 72 " model vdw 2.620 3.040 nonbonded pdb=" N SER D 90 " pdb=" O SER D 90 " model vdw 2.622 2.496 ... (remaining 52553 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: 14.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6590 Z= 0.211 Angle : 0.787 11.981 8951 Z= 0.424 Chirality : 0.051 0.279 971 Planarity : 0.007 0.070 1144 Dihedral : 13.254 89.673 2367 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.29), residues: 821 helix: None (None), residues: 0 sheet: -0.37 (0.30), residues: 302 loop : -1.00 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 774 TYR 0.029 0.002 TYR B 49 PHE 0.019 0.002 PHE A 100B TRP 0.050 0.003 TRP A 52 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 6574) covalent geometry : angle 0.78123 / 0.42 ( 8919) SS BOND : bond 0.00268 / 0.18 ( 16) SS BOND : angle 1.71910 / 1.41 ( 32) hydrogen bonds : bond 0.22423 / 14.69 ( 187) hydrogen bonds : angle 11.81772 / 8.14 ( 552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8436 (tt0) cc_final: 0.7705 (mm110) REVERT: B 45 LYS cc_start: 0.8433 (tttt) cc_final: 0.8143 (mptt) REVERT: E 108 THR cc_start: 0.7889 (m) cc_final: 0.7562 (p) REVERT: F 32 TYR cc_start: 0.8175 (m-80) cc_final: 0.7712 (m-80) REVERT: F 67 SER cc_start: 0.8693 (m) cc_final: 0.8484 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0883 time to fit residues: 21.3121 Evaluate side-chains 140 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS F 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.181544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145125 restraints weight = 8326.358| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.41 r_work: 0.3542 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6590 Z= 0.174 Angle : 0.642 10.960 8951 Z= 0.342 Chirality : 0.047 0.228 971 Planarity : 0.005 0.052 1144 Dihedral : 5.508 21.267 903 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 1.97 % Allowed : 10.28 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.29), residues: 821 helix: None (None), residues: 0 sheet: -0.30 (0.31), residues: 285 loop : -0.96 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 38 TYR 0.024 0.002 TYR B 49 PHE 0.008 0.002 PHE A 67 TRP 0.015 0.002 TRP C 36 HIS 0.005 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6574) covalent geometry : angle 0.63728 / 0.34 ( 8919) SS BOND : bond 0.00324 / 0.21 ( 16) SS BOND : angle 1.43743 / 1.11 ( 32) hydrogen bonds : bond 0.03796 / 2.68 ( 187) hydrogen bonds : angle 7.20280 / 4.97 ( 552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8582 (tt0) cc_final: 0.8057 (mm110) REVERT: A 16 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7352 (ttm-80) REVERT: A 25 SER cc_start: 0.7655 (m) cc_final: 0.7247 (p) REVERT: A 52 TRP cc_start: 0.7881 (m-90) cc_final: 0.7528 (m-90) REVERT: A 75 LYS cc_start: 0.8504 (mtpt) cc_final: 0.7908 (tttp) REVERT: C 37 VAL cc_start: 0.8446 (t) cc_final: 0.8242 (m) REVERT: F 32 TYR cc_start: 0.8303 (m-80) cc_final: 0.7764 (m-80) REVERT: F 67 SER cc_start: 0.8699 (m) cc_final: 0.8271 (p) outliers start: 14 outliers final: 9 residues processed: 166 average time/residue: 0.0797 time to fit residues: 17.6304 Evaluate side-chains 151 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82BASN F 17 GLN F 53 GLN ** G 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139813 restraints weight = 8307.140| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.36 r_work: 0.3470 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6590 Z= 0.203 Angle : 0.648 8.314 8951 Z= 0.344 Chirality : 0.046 0.154 971 Planarity : 0.005 0.047 1144 Dihedral : 5.471 20.846 903 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.33 % Favored : 93.54 % Rotamer: Outliers : 4.08 % Allowed : 12.39 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.28), residues: 821 helix: -5.14 (0.37), residues: 6 sheet: -0.25 (0.31), residues: 274 loop : -1.06 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.027 0.002 TYR B 49 PHE 0.009 0.002 PHE F 62 TRP 0.015 0.002 TRP A 103 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6574) covalent geometry : angle 0.64465 / 0.34 ( 8919) SS BOND : bond 0.00304 / 0.21 ( 16) SS BOND : angle 1.32946 / 0.99 ( 32) hydrogen bonds : bond 0.03768 / 2.68 ( 187) hydrogen bonds : angle 6.67709 / 4.62 ( 552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.246 Fit side-chains REVERT: A 13 GLN cc_start: 0.8601 (tt0) cc_final: 0.8125 (mm110) REVERT: A 16 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7370 (ttm-80) REVERT: C 37 VAL cc_start: 0.8375 (t) cc_final: 0.8115 (m) REVERT: F 67 SER cc_start: 0.8781 (m) cc_final: 0.8323 (p) REVERT: G 760 MET cc_start: 0.3720 (mmm) cc_final: 0.3117 (mmm) REVERT: G 827 ASN cc_start: 0.7730 (m-40) cc_final: 0.7476 (t0) outliers start: 29 outliers final: 20 residues processed: 162 average time/residue: 0.0758 time to fit residues: 16.3597 Evaluate side-chains 159 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain G residue 788 CYS Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139753 restraints weight = 8371.182| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.33 r_work: 0.3459 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6590 Z= 0.189 Angle : 0.639 9.725 8951 Z= 0.337 Chirality : 0.046 0.154 971 Planarity : 0.005 0.048 1144 Dihedral : 5.367 20.549 903 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 3.38 % Allowed : 14.93 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 821 helix: -4.75 (0.73), residues: 12 sheet: -0.46 (0.31), residues: 285 loop : -0.95 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 19 TYR 0.021 0.002 TYR B 49 PHE 0.013 0.002 PHE B 83 TRP 0.027 0.002 TRP E 53 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 6574) covalent geometry : angle 0.63219 / 0.33 ( 8919) SS BOND : bond 0.00328 / 0.23 ( 16) SS BOND : angle 1.71948 / 1.38 ( 32) hydrogen bonds : bond 0.03452 / 2.47 ( 187) hydrogen bonds : angle 6.35692 / 4.41 ( 552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8585 (tt0) cc_final: 0.8078 (mm110) REVERT: A 16 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7442 (ttm-80) REVERT: A 52 TRP cc_start: 0.7958 (m-90) cc_final: 0.7675 (m-90) REVERT: B 61 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7624 (ptt-90) REVERT: C 37 VAL cc_start: 0.8326 (t) cc_final: 0.8091 (m) REVERT: C 43 LYS cc_start: 0.7973 (tptt) cc_final: 0.7685 (pttt) REVERT: C 97 GLU cc_start: 0.7845 (tt0) cc_final: 0.7489 (mp0) REVERT: F 67 SER cc_start: 0.8780 (m) cc_final: 0.8416 (p) REVERT: G 760 MET cc_start: 0.3814 (mmm) cc_final: 0.3162 (mmm) outliers start: 24 outliers final: 20 residues processed: 160 average time/residue: 0.0684 time to fit residues: 14.5581 Evaluate side-chains 160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 788 CYS Chi-restraints excluded: chain G residue 838 GLU Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138102 restraints weight = 8502.700| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.35 r_work: 0.3451 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6590 Z= 0.178 Angle : 0.616 9.206 8951 Z= 0.326 Chirality : 0.046 0.198 971 Planarity : 0.005 0.046 1144 Dihedral : 5.301 19.884 903 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 4.65 % Allowed : 16.20 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.29), residues: 821 helix: -4.73 (0.75), residues: 12 sheet: -0.34 (0.31), residues: 289 loop : -0.92 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 19 TYR 0.021 0.001 TYR B 49 PHE 0.008 0.002 PHE B 83 TRP 0.012 0.002 TRP E 53 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 6574) covalent geometry : angle 0.61066 / 0.32 ( 8919) SS BOND : bond 0.00272 / 0.19 ( 16) SS BOND : angle 1.46299 / 1.14 ( 32) hydrogen bonds : bond 0.03260 / 2.30 ( 187) hydrogen bonds : angle 6.13943 / 4.28 ( 552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8579 (tt0) cc_final: 0.8047 (mm110) REVERT: A 16 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7289 (ttm-80) REVERT: A 52 TRP cc_start: 0.7924 (m-90) cc_final: 0.7576 (m-10) REVERT: B 36 TYR cc_start: 0.9091 (m-80) cc_final: 0.8660 (m-80) REVERT: C 37 VAL cc_start: 0.8251 (t) cc_final: 0.7954 (m) REVERT: C 97 GLU cc_start: 0.7849 (tt0) cc_final: 0.7475 (mp0) REVERT: F 67 SER cc_start: 0.8701 (m) cc_final: 0.8364 (p) REVERT: G 760 MET cc_start: 0.3913 (mmm) cc_final: 0.3321 (mmm) outliers start: 33 outliers final: 25 residues processed: 166 average time/residue: 0.0586 time to fit residues: 13.1584 Evaluate side-chains 163 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 838 GLU Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137651 restraints weight = 8372.656| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.18 r_work: 0.3477 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6590 Z= 0.205 Angle : 0.651 10.750 8951 Z= 0.342 Chirality : 0.046 0.201 971 Planarity : 0.005 0.046 1144 Dihedral : 5.355 19.978 903 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.04 % Favored : 91.84 % Rotamer: Outliers : 4.51 % Allowed : 17.32 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.29), residues: 821 helix: -4.71 (0.76), residues: 12 sheet: -0.24 (0.32), residues: 279 loop : -1.02 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 61 TYR 0.023 0.002 TYR B 49 PHE 0.049 0.002 PHE A 67 TRP 0.024 0.002 TRP C 103 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 6574) covalent geometry : angle 0.64663 / 0.34 ( 8919) SS BOND : bond 0.00306 / 0.21 ( 16) SS BOND : angle 1.37614 / 1.05 ( 32) hydrogen bonds : bond 0.03384 / 2.41 ( 187) hydrogen bonds : angle 6.23487 / 4.36 ( 552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8699 (tt0) cc_final: 0.8069 (mm110) REVERT: A 16 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7394 (ttm-80) REVERT: A 52 TRP cc_start: 0.8148 (m-90) cc_final: 0.7743 (m-10) REVERT: C 37 VAL cc_start: 0.8366 (t) cc_final: 0.8068 (m) REVERT: C 97 GLU cc_start: 0.8094 (tt0) cc_final: 0.7634 (mp0) REVERT: F 32 TYR cc_start: 0.8536 (m-80) cc_final: 0.7769 (m-80) REVERT: F 67 SER cc_start: 0.8764 (m) cc_final: 0.8404 (p) REVERT: G 760 MET cc_start: 0.4135 (mmm) cc_final: 0.3553 (mmm) outliers start: 32 outliers final: 28 residues processed: 166 average time/residue: 0.0767 time to fit residues: 17.1413 Evaluate side-chains 169 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 838 GLU Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN C 105 GLN E 82BASN E 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138436 restraints weight = 8425.868| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.09 r_work: 0.3458 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6590 Z= 0.163 Angle : 0.633 12.360 8951 Z= 0.330 Chirality : 0.046 0.206 971 Planarity : 0.005 0.045 1144 Dihedral : 5.267 20.041 903 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 3.66 % Allowed : 19.15 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.29), residues: 821 helix: -4.72 (0.75), residues: 12 sheet: -0.18 (0.32), residues: 282 loop : -0.99 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 61 TYR 0.020 0.001 TYR B 49 PHE 0.028 0.002 PHE A 67 TRP 0.029 0.002 TRP C 103 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6574) covalent geometry : angle 0.63007 / 0.33 ( 8919) SS BOND : bond 0.00210 / 0.15 ( 16) SS BOND : angle 1.24766 / 0.96 ( 32) hydrogen bonds : bond 0.03101 / 2.19 ( 187) hydrogen bonds : angle 6.02143 / 4.20 ( 552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.229 Fit side-chains REVERT: A 13 GLN cc_start: 0.8681 (tt0) cc_final: 0.8195 (mm110) REVERT: A 16 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7405 (ttm-80) REVERT: C 37 VAL cc_start: 0.8308 (t) cc_final: 0.8061 (m) REVERT: C 97 GLU cc_start: 0.7987 (tt0) cc_final: 0.7666 (mp0) REVERT: F 32 TYR cc_start: 0.8404 (m-80) cc_final: 0.7716 (m-80) REVERT: F 67 SER cc_start: 0.8704 (m) cc_final: 0.8386 (p) REVERT: G 760 MET cc_start: 0.4140 (mmm) cc_final: 0.3615 (mmm) outliers start: 26 outliers final: 21 residues processed: 160 average time/residue: 0.0757 time to fit residues: 16.2243 Evaluate side-chains 159 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 838 GLU Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82BASN F 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133484 restraints weight = 8480.781| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.10 r_work: 0.3427 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6590 Z= 0.192 Angle : 0.656 11.178 8951 Z= 0.341 Chirality : 0.046 0.214 971 Planarity : 0.005 0.045 1144 Dihedral : 5.314 20.075 903 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.53 % Favored : 91.35 % Rotamer: Outliers : 3.94 % Allowed : 19.15 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.29), residues: 821 helix: -4.52 (0.95), residues: 12 sheet: -0.20 (0.32), residues: 280 loop : -1.00 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 61 TYR 0.023 0.002 TYR B 49 PHE 0.026 0.002 PHE A 67 TRP 0.047 0.002 TRP E 53 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 6574) covalent geometry : angle 0.65307 / 0.34 ( 8919) SS BOND : bond 0.00288 / 0.20 ( 16) SS BOND : angle 1.26054 / 0.96 ( 32) hydrogen bonds : bond 0.03252 / 2.32 ( 187) hydrogen bonds : angle 6.09689 / 4.25 ( 552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8660 (tt0) cc_final: 0.8167 (mm110) REVERT: A 16 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7509 (ttm-80) REVERT: C 37 VAL cc_start: 0.8410 (t) cc_final: 0.8169 (m) REVERT: C 97 GLU cc_start: 0.8019 (tt0) cc_final: 0.7664 (mp0) REVERT: D 61 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.7214 (ttp-110) REVERT: F 67 SER cc_start: 0.8796 (m) cc_final: 0.8490 (p) REVERT: F 92 ASP cc_start: 0.7480 (t70) cc_final: 0.6774 (t70) REVERT: G 760 MET cc_start: 0.4147 (mmm) cc_final: 0.3801 (mmm) outliers start: 28 outliers final: 24 residues processed: 163 average time/residue: 0.0712 time to fit residues: 15.5547 Evaluate side-chains 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 ASN C 81 GLN D 79 GLN E 82BASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128496 restraints weight = 8637.490| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.26 r_work: 0.3357 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6590 Z= 0.249 Angle : 0.717 11.035 8951 Z= 0.369 Chirality : 0.048 0.210 971 Planarity : 0.005 0.043 1144 Dihedral : 5.560 21.452 903 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.26 % Favored : 90.62 % Rotamer: Outliers : 4.51 % Allowed : 19.86 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.29), residues: 821 helix: -4.50 (0.96), residues: 12 sheet: -0.43 (0.31), residues: 287 loop : -1.00 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 61 TYR 0.028 0.002 TYR B 49 PHE 0.033 0.002 PHE A 67 TRP 0.043 0.003 TRP E 53 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 ( 6574) covalent geometry : angle 0.71369 / 0.37 ( 8919) SS BOND : bond 0.00418 / 0.27 ( 16) SS BOND : angle 1.36618 / 1.02 ( 32) hydrogen bonds : bond 0.03598 / 2.60 ( 187) hydrogen bonds : angle 6.40804 / 4.49 ( 552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8669 (tt0) cc_final: 0.8074 (mm110) REVERT: A 16 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7294 (ttm-80) REVERT: C 37 VAL cc_start: 0.8544 (t) cc_final: 0.8327 (m) REVERT: C 82 MET cc_start: 0.5149 (mtt) cc_final: 0.4901 (mtm) REVERT: C 97 GLU cc_start: 0.8145 (tt0) cc_final: 0.7726 (mp0) REVERT: F 67 SER cc_start: 0.8834 (m) cc_final: 0.8387 (p) REVERT: F 79 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7408 (mmt-90) REVERT: F 92 ASP cc_start: 0.7801 (t70) cc_final: 0.7109 (t70) REVERT: G 760 MET cc_start: 0.4398 (mmm) cc_final: 0.4041 (mmm) outliers start: 32 outliers final: 29 residues processed: 168 average time/residue: 0.0777 time to fit residues: 18.0256 Evaluate side-chains 172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 808 SER Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN D 89 GLN E 82BASN G 849 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140706 restraints weight = 8297.541| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.03 r_work: 0.3515 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6590 Z= 0.138 Angle : 0.666 10.475 8951 Z= 0.345 Chirality : 0.046 0.202 971 Planarity : 0.005 0.045 1144 Dihedral : 5.422 23.238 903 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.16 % Favored : 91.72 % Rotamer: Outliers : 2.96 % Allowed : 21.97 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.29), residues: 821 helix: -4.89 (0.59), residues: 12 sheet: -0.33 (0.31), residues: 290 loop : -0.90 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 18 TYR 0.016 0.001 TYR B 49 PHE 0.029 0.002 PHE A 67 TRP 0.043 0.003 TRP C 103 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6574) covalent geometry : angle 0.66360 / 0.34 ( 8919) SS BOND : bond 0.00238 / 0.16 ( 16) SS BOND : angle 1.12298 / 0.89 ( 32) hydrogen bonds : bond 0.03104 / 2.23 ( 187) hydrogen bonds : angle 5.95160 / 4.15 ( 552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.269 Fit side-chains REVERT: A 13 GLN cc_start: 0.8545 (tt0) cc_final: 0.8099 (mm110) REVERT: A 16 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7535 (ttm-80) REVERT: B 36 TYR cc_start: 0.9022 (m-80) cc_final: 0.8638 (m-80) REVERT: C 97 GLU cc_start: 0.7946 (tt0) cc_final: 0.7570 (mp0) REVERT: F 67 SER cc_start: 0.8710 (m) cc_final: 0.8287 (p) REVERT: F 79 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7268 (mmt-90) REVERT: F 92 ASP cc_start: 0.7409 (t70) cc_final: 0.6625 (t70) REVERT: G 760 MET cc_start: 0.4049 (mmm) cc_final: 0.3735 (mmm) outliers start: 21 outliers final: 19 residues processed: 157 average time/residue: 0.0638 time to fit residues: 13.7432 Evaluate side-chains 156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain G residue 808 SER Chi-restraints excluded: chain G residue 840 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136920 restraints weight = 8385.500| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.07 r_work: 0.3457 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6590 Z= 0.173 Angle : 0.678 10.380 8951 Z= 0.349 Chirality : 0.047 0.216 971 Planarity : 0.005 0.047 1144 Dihedral : 5.373 21.504 903 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 2.96 % Allowed : 22.68 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.29), residues: 821 helix: -5.18 (0.34), residues: 12 sheet: -0.41 (0.31), residues: 285 loop : -0.92 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.022 0.002 TYR B 49 PHE 0.029 0.002 PHE A 67 TRP 0.045 0.003 TRP E 53 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6574) covalent geometry : angle 0.67544 / 0.35 ( 8919) SS BOND : bond 0.00293 / 0.20 ( 16) SS BOND : angle 1.19783 / 0.93 ( 32) hydrogen bonds : bond 0.03153 / 2.26 ( 187) hydrogen bonds : angle 5.95052 / 4.15 ( 552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.22 seconds wall clock time: 35 minutes 30.32 seconds (2130.32 seconds total)