Starting phenix.real_space_refine on Thu Feb 13 17:20:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4h_30078/02_2025/6m4h_30078.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 206 5.49 5 S 16 5.16 5 C 5279 2.51 5 N 1735 2.21 5 O 2184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9420 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2132 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2090 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Time building chain proxies: 5.75, per 1000 atoms: 0.61 Number of scatterers: 9420 At special positions: 0 Unit cell: (97.76, 114.4, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 206 15.00 O 2184 8.00 N 1735 7.00 C 5279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 706.4 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 74.7% alpha, 2.1% beta 98 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.585A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.635A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 52 through 78 removed outlier: 3.865A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.786A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 50 through 76 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.788A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 93 " --> pdb=" O MET G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.702A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.027A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.729A pdb=" N THR C 105 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.123A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 316 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 3.12 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: 1574 1.33 - 1.45: 3361 1.45 - 1.57: 4624 1.57 - 1.69: 412 1.69 - 1.80: 28 Bond restraints: 9999 Sorted by residual: bond pdb=" C ARG G 49 " pdb=" N THR G 50 " ideal model delta sigma weight residual 1.333 1.287 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N GLU G 79 " pdb=" CA GLU G 79 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.16e-02 7.43e+03 8.37e+00 bond pdb=" N SER G 77 " pdb=" CA SER G 77 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.31e+00 bond pdb=" N SER C 77 " pdb=" CA SER C 77 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 ... (remaining 9994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 14258 3.12 - 6.24: 126 6.24 - 9.36: 10 9.36 - 12.48: 0 12.48 - 15.60: 1 Bond angle restraints: 14395 Sorted by residual: angle pdb=" N ASN G 76 " pdb=" CA ASN G 76 " pdb=" C ASN G 76 " ideal model delta sigma weight residual 113.37 106.59 6.78 1.38e+00 5.25e-01 2.41e+01 angle pdb=" C ASN G 76 " pdb=" N SER G 77 " pdb=" CA SER G 77 " ideal model delta sigma weight residual 121.87 129.48 -7.61 1.64e+00 3.72e-01 2.15e+01 angle pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " pdb=" CD GLU F 53 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.70e+00 3.46e-01 1.78e+01 angle pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" C CYS E 96 " pdb=" N GLU E 97 " pdb=" CA GLU E 97 " ideal model delta sigma weight residual 120.68 113.87 6.81 1.70e+00 3.46e-01 1.60e+01 ... (remaining 14390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 4392 35.17 - 70.34: 1018 70.34 - 105.51: 46 105.51 - 140.69: 4 140.69 - 175.86: 6 Dihedral angle restraints: 5466 sinusoidal: 3548 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DC I 34 " pdb=" C3' DC I 34 " pdb=" O3' DC I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual -140.00 35.86 -175.86 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual -140.00 32.37 -172.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA HIS G 92 " pdb=" C HIS G 92 " pdb=" N ASN G 93 " pdb=" CA ASN G 93 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 962 0.035 - 0.071: 491 0.071 - 0.106: 156 0.106 - 0.141: 45 0.141 - 0.176: 12 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA GLU A 97 " pdb=" N GLU A 97 " pdb=" C GLU A 97 " pdb=" CB GLU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU F 52 " pdb=" N GLU F 52 " pdb=" C GLU F 52 " pdb=" CB GLU F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA GLU E 97 " pdb=" N GLU E 97 " pdb=" C GLU E 97 " pdb=" CB GLU E 97 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 1663 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 51 " -0.099 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO C 52 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 67 " 0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C ASN D 67 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN D 67 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 67 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN H 67 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN H 67 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP H 68 " -0.024 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 33 2.36 - 3.00: 4572 3.00 - 3.63: 17703 3.63 - 4.27: 25383 4.27 - 4.90: 36252 Nonbonded interactions: 83943 Sorted by model distance: nonbonded pdb=" OP1 DT J 31 " pdb=" OG SER C 20 " model vdw 1.729 3.040 nonbonded pdb=" OP1 DT J 31 " pdb=" CA SER C 20 " model vdw 1.765 3.470 nonbonded pdb=" OP2 DC I 81 " pdb=" N GLY B 48 " model vdw 1.880 3.120 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 1.970 3.120 nonbonded pdb=" OP2 DA I 113 " pdb=" NH2 ARG C 39 " model vdw 1.974 3.120 ... (remaining 83938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue 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: 0.870 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.140 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.008 0.056 9999 Z= 0.406 Angle : 0.894 15.598 14395 Z= 0.532 Chirality : 0.048 0.176 1666 Planarity : 0.010 0.153 1100 Dihedral : 29.217 175.856 4222 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 2.85 % Allowed : 2.31 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.19), residues: 640 helix: -4.08 (0.11), residues: 444 sheet: None (None), residues: 0 loop : -3.15 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.021 0.003 PHE E 67 TYR 0.026 0.003 TYR B 51 ARG 0.006 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8298 (m) REVERT: B 59 LYS cc_start: 0.8613 (tttt) cc_final: 0.8119 (ttmt) REVERT: B 75 HIS cc_start: 0.7843 (t-90) cc_final: 0.7516 (t-170) REVERT: B 80 THR cc_start: 0.7724 (m) cc_final: 0.7488 (p) REVERT: B 84 MET cc_start: 0.6505 (mmm) cc_final: 0.5995 (mmm) REVERT: C 68 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 62 MET cc_start: 0.8518 (mmm) cc_final: 0.8317 (mmt) REVERT: D 68 ASP cc_start: 0.7408 (t70) cc_final: 0.7073 (t0) REVERT: D 70 PHE cc_start: 0.8359 (t80) cc_final: 0.8127 (t80) REVERT: D 102 LEU cc_start: 0.8193 (mp) cc_final: 0.7980 (mp) REVERT: E 101 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (m) REVERT: F 29 ILE cc_start: 0.8917 (mm) cc_final: 0.8632 (mm) REVERT: F 59 LYS cc_start: 0.8493 (tttt) cc_final: 0.8097 (tttp) REVERT: F 75 HIS cc_start: 0.7852 (t-90) cc_final: 0.7430 (t70) REVERT: G 31 VAL cc_start: 0.7902 (m) cc_final: 0.7430 (p) REVERT: H 37 TYR cc_start: 0.5303 (m-10) cc_final: 0.4674 (m-80) REVERT: H 62 MET cc_start: 0.8383 (mmm) cc_final: 0.8092 (mmt) REVERT: H 68 ASP cc_start: 0.7535 (t70) cc_final: 0.7027 (t0) outliers start: 16 outliers final: 2 residues processed: 292 average time/residue: 0.3431 time to fit residues: 122.8624 Evaluate side-chains 153 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 72 ASN D 82 HIS E 68 GLN G 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036903 restraints weight = 64919.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038044 restraints weight = 30779.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038790 restraints weight = 19555.467| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9999 Z= 0.222 Angle : 0.716 10.139 14395 Z= 0.414 Chirality : 0.040 0.157 1666 Planarity : 0.006 0.056 1100 Dihedral : 33.513 171.000 2966 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 17.79 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.28), residues: 640 helix: -1.45 (0.20), residues: 472 sheet: None (None), residues: 0 loop : -2.42 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE A 78 TYR 0.018 0.002 TYR H 37 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.9016 (mt0) cc_final: 0.8604 (mt0) REVERT: A 86 SER cc_start: 0.8940 (t) cc_final: 0.8459 (m) REVERT: B 59 LYS cc_start: 0.9221 (tttt) cc_final: 0.8743 (tptm) REVERT: B 63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 80 THR cc_start: 0.8842 (m) cc_final: 0.8458 (p) REVERT: C 31 VAL cc_start: 0.8818 (m) cc_final: 0.8142 (p) REVERT: C 33 GLN cc_start: 0.8932 (tt0) cc_final: 0.8200 (tm-30) REVERT: C 63 THR cc_start: 0.9227 (m) cc_final: 0.8894 (p) REVERT: C 68 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 72 ASN cc_start: 0.8354 (m-40) cc_final: 0.7898 (m-40) REVERT: C 80 ARG cc_start: 0.7010 (tpm170) cc_final: 0.6692 (tpt90) REVERT: D 40 TYR cc_start: 0.8901 (m-80) cc_final: 0.8466 (m-80) REVERT: D 80 LEU cc_start: 0.8841 (mp) cc_final: 0.8315 (tp) REVERT: D 93 GLU cc_start: 0.8496 (mp0) cc_final: 0.8100 (mm-30) REVERT: D 105 GLU cc_start: 0.8632 (pm20) cc_final: 0.8399 (pm20) REVERT: E 61 LEU cc_start: 0.8725 (mt) cc_final: 0.8254 (mp) REVERT: E 85 GLN cc_start: 0.8976 (mt0) cc_final: 0.8586 (mt0) REVERT: E 86 SER cc_start: 0.8961 (t) cc_final: 0.8504 (m) REVERT: F 59 LYS cc_start: 0.9249 (tttt) cc_final: 0.8930 (tttp) REVERT: F 75 HIS cc_start: 0.8555 (t-90) cc_final: 0.8243 (t-170) REVERT: F 92 ARG cc_start: 0.8478 (ttm110) cc_final: 0.7961 (tpp80) REVERT: G 31 VAL cc_start: 0.8717 (m) cc_final: 0.8149 (p) REVERT: H 93 GLU cc_start: 0.8532 (mp0) cc_final: 0.8104 (mm-30) REVERT: H 100 LEU cc_start: 0.9117 (mt) cc_final: 0.8718 (mt) outliers start: 17 outliers final: 6 residues processed: 199 average time/residue: 0.2945 time to fit residues: 74.7531 Evaluate side-chains 162 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 84 ASN E 93 GLN G 45 GLN H 49 HIS H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035483 restraints weight = 66573.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036586 restraints weight = 32659.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037293 restraints weight = 20991.918| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9999 Z= 0.250 Angle : 0.691 6.163 14395 Z= 0.402 Chirality : 0.040 0.162 1666 Planarity : 0.005 0.049 1100 Dihedral : 33.406 176.079 2962 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.20 % Allowed : 20.46 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.31), residues: 640 helix: 0.27 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -2.22 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 82 PHE 0.008 0.001 PHE G 101 TYR 0.019 0.002 TYR G 61 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 86 SER cc_start: 0.9034 (t) cc_final: 0.8549 (m) REVERT: A 90 MET cc_start: 0.9027 (mmm) cc_final: 0.8645 (mmp) REVERT: A 126 LEU cc_start: 0.9135 (tt) cc_final: 0.8926 (tt) REVERT: B 80 THR cc_start: 0.8999 (m) cc_final: 0.8537 (p) REVERT: C 31 VAL cc_start: 0.9019 (m) cc_final: 0.8627 (p) REVERT: C 33 GLN cc_start: 0.8994 (tt0) cc_final: 0.8301 (tm-30) REVERT: C 63 THR cc_start: 0.9300 (m) cc_final: 0.9014 (p) REVERT: C 68 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 76 ASN cc_start: 0.8965 (p0) cc_final: 0.8412 (p0) REVERT: D 80 LEU cc_start: 0.9140 (mp) cc_final: 0.8648 (mm) REVERT: E 68 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8483 (tp-100) REVERT: E 69 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7947 (mtm110) REVERT: E 86 SER cc_start: 0.9014 (t) cc_final: 0.8548 (m) REVERT: E 90 MET cc_start: 0.9025 (mmm) cc_final: 0.8753 (mmp) REVERT: E 97 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7496 (mt-10) REVERT: F 59 LYS cc_start: 0.9306 (tttt) cc_final: 0.9021 (tttp) REVERT: F 75 HIS cc_start: 0.8513 (t-90) cc_final: 0.8104 (t-170) REVERT: F 84 MET cc_start: 0.8541 (tpp) cc_final: 0.8311 (tpp) REVERT: F 88 TYR cc_start: 0.9028 (m-80) cc_final: 0.8810 (m-80) REVERT: G 31 VAL cc_start: 0.9092 (m) cc_final: 0.8593 (p) REVERT: G 60 GLU cc_start: 0.9055 (tt0) cc_final: 0.7864 (tt0) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 0.2761 time to fit residues: 61.8477 Evaluate side-chains 151 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 68 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.046220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.035388 restraints weight = 65602.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036495 restraints weight = 30712.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037204 restraints weight = 19319.397| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9999 Z= 0.251 Angle : 0.680 6.162 14395 Z= 0.394 Chirality : 0.039 0.161 1666 Planarity : 0.005 0.041 1100 Dihedral : 33.332 177.556 2962 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 21.71 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.33), residues: 640 helix: 0.89 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.06 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 49 PHE 0.007 0.001 PHE D 70 TYR 0.013 0.002 TYR C 61 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8678 (mm) cc_final: 0.8402 (mp) REVERT: A 69 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: A 86 SER cc_start: 0.9171 (t) cc_final: 0.8743 (m) REVERT: A 90 MET cc_start: 0.9002 (mmm) cc_final: 0.8635 (mmp) REVERT: B 80 THR cc_start: 0.9084 (m) cc_final: 0.8606 (p) REVERT: C 31 VAL cc_start: 0.9165 (m) cc_final: 0.8588 (p) REVERT: C 33 GLN cc_start: 0.9062 (tt0) cc_final: 0.8547 (tm-30) REVERT: C 61 TYR cc_start: 0.8547 (t80) cc_final: 0.8069 (t80) REVERT: C 63 THR cc_start: 0.9371 (m) cc_final: 0.9116 (p) REVERT: C 68 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 40 TYR cc_start: 0.8758 (m-80) cc_final: 0.8396 (m-80) REVERT: D 99 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8082 (mpp80) REVERT: E 68 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8505 (tp-100) REVERT: E 69 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7784 (mtm-85) REVERT: E 86 SER cc_start: 0.9113 (t) cc_final: 0.8696 (m) REVERT: E 90 MET cc_start: 0.9016 (mmm) cc_final: 0.8693 (mmp) REVERT: E 125 GLN cc_start: 0.9135 (mt0) cc_final: 0.8912 (mt0) REVERT: F 59 LYS cc_start: 0.9307 (tttt) cc_final: 0.9039 (tttp) REVERT: F 84 MET cc_start: 0.8677 (tpp) cc_final: 0.8442 (tpp) REVERT: G 31 VAL cc_start: 0.9249 (m) cc_final: 0.8769 (p) REVERT: G 60 GLU cc_start: 0.9169 (tt0) cc_final: 0.7883 (tt0) REVERT: H 93 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8286 (mm-30) outliers start: 19 outliers final: 13 residues processed: 164 average time/residue: 0.2876 time to fit residues: 60.6879 Evaluate side-chains 152 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.047478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036469 restraints weight = 66062.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037557 restraints weight = 31665.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038268 restraints weight = 20273.984| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9999 Z= 0.194 Angle : 0.657 9.911 14395 Z= 0.378 Chirality : 0.038 0.169 1666 Planarity : 0.004 0.043 1100 Dihedral : 33.068 177.065 2962 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.38 % Allowed : 22.42 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.33), residues: 640 helix: 1.44 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 49 PHE 0.006 0.001 PHE A 78 TYR 0.018 0.002 TYR G 61 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7582 (mtm-85) REVERT: A 86 SER cc_start: 0.9102 (t) cc_final: 0.8679 (m) REVERT: A 90 MET cc_start: 0.9000 (mmm) cc_final: 0.8656 (mmp) REVERT: A 126 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8634 (tp) REVERT: B 75 HIS cc_start: 0.8607 (t70) cc_final: 0.8092 (t-170) REVERT: B 80 THR cc_start: 0.9041 (m) cc_final: 0.8555 (p) REVERT: C 31 VAL cc_start: 0.9119 (m) cc_final: 0.8489 (p) REVERT: C 33 GLN cc_start: 0.9016 (tt0) cc_final: 0.8579 (tm-30) REVERT: C 35 GLU cc_start: 0.9406 (tt0) cc_final: 0.9127 (tt0) REVERT: C 60 GLU cc_start: 0.8743 (tt0) cc_final: 0.8462 (tt0) REVERT: C 63 THR cc_start: 0.9355 (m) cc_final: 0.9043 (p) REVERT: C 68 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 40 TYR cc_start: 0.8643 (m-80) cc_final: 0.8335 (m-80) REVERT: D 93 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7286 (tp30) REVERT: E 69 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7399 (mtm-85) REVERT: E 86 SER cc_start: 0.9062 (t) cc_final: 0.8657 (m) REVERT: E 90 MET cc_start: 0.8947 (mmm) cc_final: 0.8629 (mmp) REVERT: F 59 LYS cc_start: 0.9319 (tttt) cc_final: 0.9069 (tttp) REVERT: G 31 VAL cc_start: 0.9192 (m) cc_final: 0.8702 (p) REVERT: G 60 GLU cc_start: 0.9137 (tt0) cc_final: 0.7871 (tt0) REVERT: G 68 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8183 (pp20) REVERT: H 93 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8233 (mm-30) REVERT: H 99 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8067 (mtm180) outliers start: 19 outliers final: 10 residues processed: 167 average time/residue: 0.2677 time to fit residues: 58.3909 Evaluate side-chains 152 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 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 = 0.3286 r_free = 0.3286 target = 0.046648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035552 restraints weight = 66205.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036623 restraints weight = 32674.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037331 restraints weight = 21125.936| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9999 Z= 0.235 Angle : 0.671 9.978 14395 Z= 0.382 Chirality : 0.038 0.164 1666 Planarity : 0.004 0.044 1100 Dihedral : 32.989 176.752 2962 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.02 % Allowed : 24.91 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.33), residues: 640 helix: 1.64 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.005 0.001 PHE D 70 TYR 0.018 0.002 TYR G 61 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.9214 (t) cc_final: 0.8812 (m) REVERT: A 90 MET cc_start: 0.9031 (mmm) cc_final: 0.8665 (mmp) REVERT: B 75 HIS cc_start: 0.8544 (t70) cc_final: 0.8176 (t-170) REVERT: B 80 THR cc_start: 0.9093 (m) cc_final: 0.8773 (p) REVERT: C 31 VAL cc_start: 0.9275 (m) cc_final: 0.8684 (p) REVERT: C 33 GLN cc_start: 0.9047 (tt0) cc_final: 0.8669 (tm-30) REVERT: C 35 GLU cc_start: 0.9441 (tt0) cc_final: 0.9201 (tt0) REVERT: C 63 THR cc_start: 0.9428 (m) cc_final: 0.9200 (p) REVERT: C 68 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 40 TYR cc_start: 0.8626 (m-80) cc_final: 0.8244 (m-80) REVERT: E 90 MET cc_start: 0.9021 (mmm) cc_final: 0.8670 (mmp) REVERT: F 59 LYS cc_start: 0.9335 (tttt) cc_final: 0.9079 (tttp) REVERT: F 84 MET cc_start: 0.8687 (tpp) cc_final: 0.8376 (tpp) REVERT: F 88 TYR cc_start: 0.9073 (m-80) cc_final: 0.8873 (m-80) REVERT: G 31 VAL cc_start: 0.9306 (m) cc_final: 0.8866 (p) REVERT: G 60 GLU cc_start: 0.9189 (tt0) cc_final: 0.7910 (tt0) REVERT: G 68 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8130 (pp20) REVERT: H 61 ILE cc_start: 0.9142 (mm) cc_final: 0.8916 (mm) REVERT: H 93 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8374 (mm-30) REVERT: H 99 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7744 (mtm180) outliers start: 17 outliers final: 12 residues processed: 152 average time/residue: 0.2519 time to fit residues: 50.7408 Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.036298 restraints weight = 66375.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037389 restraints weight = 32452.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038115 restraints weight = 20832.316| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9999 Z= 0.205 Angle : 0.659 8.591 14395 Z= 0.376 Chirality : 0.038 0.188 1666 Planarity : 0.004 0.041 1100 Dihedral : 32.813 175.209 2962 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.31 % Allowed : 25.98 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.33), residues: 640 helix: 1.71 (0.24), residues: 478 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.005 0.001 PHE D 70 TYR 0.034 0.002 TYR B 88 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7605 (mtm-85) REVERT: A 90 MET cc_start: 0.8961 (mmm) cc_final: 0.8589 (mmp) REVERT: A 125 GLN cc_start: 0.9190 (mt0) cc_final: 0.8965 (mp10) REVERT: B 75 HIS cc_start: 0.8624 (t70) cc_final: 0.8217 (t-170) REVERT: B 80 THR cc_start: 0.9082 (m) cc_final: 0.8689 (p) REVERT: C 31 VAL cc_start: 0.9247 (m) cc_final: 0.8623 (p) REVERT: C 33 GLN cc_start: 0.9035 (tt0) cc_final: 0.8611 (tm-30) REVERT: C 35 GLU cc_start: 0.9432 (tt0) cc_final: 0.9169 (tt0) REVERT: C 42 HIS cc_start: 0.8750 (m90) cc_final: 0.8474 (m90) REVERT: C 63 THR cc_start: 0.9392 (m) cc_final: 0.9099 (p) REVERT: C 68 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 40 TYR cc_start: 0.8567 (m-80) cc_final: 0.8255 (m-80) REVERT: E 90 MET cc_start: 0.8962 (mmm) cc_final: 0.8607 (mmp) REVERT: F 59 LYS cc_start: 0.9314 (tttt) cc_final: 0.9078 (tttp) REVERT: G 31 VAL cc_start: 0.9274 (m) cc_final: 0.8809 (p) REVERT: G 60 GLU cc_start: 0.9117 (tt0) cc_final: 0.7929 (tt0) REVERT: H 61 ILE cc_start: 0.9149 (mm) cc_final: 0.8937 (mm) REVERT: H 93 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8232 (tp30) REVERT: H 99 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7733 (mtm180) outliers start: 13 outliers final: 9 residues processed: 153 average time/residue: 0.2972 time to fit residues: 58.4093 Evaluate side-chains 146 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 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 = 0.3305 r_free = 0.3305 target = 0.047094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036026 restraints weight = 67924.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037109 restraints weight = 33640.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037819 restraints weight = 21778.131| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9999 Z= 0.218 Angle : 0.665 8.402 14395 Z= 0.379 Chirality : 0.038 0.181 1666 Planarity : 0.004 0.040 1100 Dihedral : 32.830 174.279 2962 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.20 % Allowed : 25.44 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.33), residues: 640 helix: 1.77 (0.24), residues: 478 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.018 0.001 PHE H 70 TYR 0.036 0.002 TYR B 88 ARG 0.007 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7429 (mtm-85) REVERT: A 90 MET cc_start: 0.8949 (mmm) cc_final: 0.8564 (mmp) REVERT: B 80 THR cc_start: 0.9096 (m) cc_final: 0.8777 (p) REVERT: C 31 VAL cc_start: 0.9299 (m) cc_final: 0.8720 (p) REVERT: C 33 GLN cc_start: 0.9042 (tt0) cc_final: 0.8624 (tm-30) REVERT: C 35 GLU cc_start: 0.9426 (tt0) cc_final: 0.9150 (tt0) REVERT: C 40 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 42 HIS cc_start: 0.8720 (m90) cc_final: 0.8442 (m90) REVERT: C 63 THR cc_start: 0.9409 (m) cc_final: 0.9135 (p) REVERT: C 68 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 99 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7801 (mtm-85) REVERT: E 90 MET cc_start: 0.8973 (mmm) cc_final: 0.8604 (mmp) REVERT: F 59 LYS cc_start: 0.9326 (tttt) cc_final: 0.9081 (tttp) REVERT: F 84 MET cc_start: 0.8612 (tpp) cc_final: 0.8399 (tpp) REVERT: G 31 VAL cc_start: 0.9305 (m) cc_final: 0.8847 (p) REVERT: G 60 GLU cc_start: 0.9139 (tt0) cc_final: 0.7962 (tt0) REVERT: G 68 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: H 61 ILE cc_start: 0.9128 (mm) cc_final: 0.8913 (mm) REVERT: H 93 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8248 (tp30) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.2558 time to fit residues: 49.5292 Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036552 restraints weight = 65890.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037624 restraints weight = 32649.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.038332 restraints weight = 21104.925| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9999 Z= 0.207 Angle : 0.666 8.168 14395 Z= 0.378 Chirality : 0.038 0.201 1666 Planarity : 0.004 0.041 1100 Dihedral : 32.767 173.282 2962 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.49 % Allowed : 26.51 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 640 helix: 1.75 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.005 0.001 PHE D 70 TYR 0.037 0.002 TYR B 88 ARG 0.006 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7627 (mtm-85) REVERT: A 90 MET cc_start: 0.8932 (mmm) cc_final: 0.8547 (mmp) REVERT: B 80 THR cc_start: 0.9090 (m) cc_final: 0.8768 (p) REVERT: C 31 VAL cc_start: 0.9245 (m) cc_final: 0.8636 (p) REVERT: C 33 GLN cc_start: 0.9021 (tt0) cc_final: 0.8654 (tm-30) REVERT: C 35 GLU cc_start: 0.9423 (tt0) cc_final: 0.9155 (tt0) REVERT: C 42 HIS cc_start: 0.8713 (m90) cc_final: 0.8441 (m90) REVERT: C 63 THR cc_start: 0.9393 (m) cc_final: 0.9100 (p) REVERT: C 68 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 40 TYR cc_start: 0.8459 (m-80) cc_final: 0.8184 (m-80) REVERT: D 99 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7862 (mtm-85) REVERT: E 90 MET cc_start: 0.8928 (mmm) cc_final: 0.8573 (mmp) REVERT: F 59 LYS cc_start: 0.9320 (tttt) cc_final: 0.9091 (tttp) REVERT: F 84 MET cc_start: 0.8634 (tpp) cc_final: 0.8425 (tpp) REVERT: G 31 VAL cc_start: 0.9270 (m) cc_final: 0.8801 (p) REVERT: G 60 GLU cc_start: 0.9125 (tt0) cc_final: 0.7933 (tt0) REVERT: H 61 ILE cc_start: 0.9122 (mm) cc_final: 0.8915 (mm) REVERT: H 93 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8283 (tp30) REVERT: H 95 GLN cc_start: 0.8098 (tt0) cc_final: 0.7685 (tt0) outliers start: 14 outliers final: 11 residues processed: 149 average time/residue: 0.2686 time to fit residues: 52.3589 Evaluate side-chains 145 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 57 optimal weight: 0.0770 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.047977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036939 restraints weight = 67226.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038023 restraints weight = 33296.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038741 restraints weight = 21626.010| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9999 Z= 0.199 Angle : 0.666 8.196 14395 Z= 0.379 Chirality : 0.038 0.186 1666 Planarity : 0.005 0.056 1100 Dihedral : 32.697 170.773 2962 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.31 % Allowed : 27.22 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.33), residues: 640 helix: 1.74 (0.23), residues: 478 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.005 0.001 PHE D 70 TYR 0.037 0.002 TYR B 88 ARG 0.005 0.000 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7476 (mtm-85) REVERT: A 90 MET cc_start: 0.8918 (mmm) cc_final: 0.8587 (mmp) REVERT: B 80 THR cc_start: 0.9071 (m) cc_final: 0.8642 (p) REVERT: B 84 MET cc_start: 0.8491 (tpp) cc_final: 0.8242 (tpp) REVERT: C 31 VAL cc_start: 0.9227 (m) cc_final: 0.8612 (p) REVERT: C 33 GLN cc_start: 0.8997 (tt0) cc_final: 0.8650 (tm-30) REVERT: C 35 GLU cc_start: 0.9426 (tt0) cc_final: 0.9178 (tt0) REVERT: C 42 HIS cc_start: 0.8702 (m90) cc_final: 0.8467 (m90) REVERT: C 63 THR cc_start: 0.9377 (m) cc_final: 0.9072 (p) REVERT: C 68 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 40 TYR cc_start: 0.8411 (m-80) cc_final: 0.8154 (m-80) REVERT: D 99 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7818 (mtm-85) REVERT: E 90 MET cc_start: 0.8912 (mmm) cc_final: 0.8558 (mmp) REVERT: F 59 LYS cc_start: 0.9302 (tttt) cc_final: 0.9070 (tttp) REVERT: G 31 VAL cc_start: 0.9243 (m) cc_final: 0.8760 (p) REVERT: G 60 GLU cc_start: 0.9112 (tt0) cc_final: 0.7906 (tt0) REVERT: H 61 ILE cc_start: 0.9109 (mm) cc_final: 0.8894 (mm) REVERT: H 93 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8236 (tp30) REVERT: H 99 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7902 (mpp80) outliers start: 13 outliers final: 9 residues processed: 148 average time/residue: 0.3039 time to fit residues: 58.3007 Evaluate side-chains 141 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 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 = 0.3328 r_free = 0.3328 target = 0.047904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036769 restraints weight = 66212.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037842 restraints weight = 33121.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038523 restraints weight = 21559.333| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9999 Z= 0.225 Angle : 0.678 8.236 14395 Z= 0.385 Chirality : 0.038 0.193 1666 Planarity : 0.005 0.062 1100 Dihedral : 32.693 170.475 2962 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.96 % Allowed : 27.76 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.33), residues: 640 helix: 1.70 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.47 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.019 0.001 PHE H 70 TYR 0.022 0.002 TYR G 61 ARG 0.010 0.000 ARG C 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.30 seconds wall clock time: 49 minutes 49.85 seconds (2989.85 seconds total)