Starting phenix.real_space_refine on Tue Jun 10 11:29:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.map" model { file = "/net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qaj_52975/06_2025/9qaj_52975.cif" } resolution = 2.95 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= 0.002 sd= 0.013 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 288 5.49 5 S 12 5.16 5 C 6714 2.51 5 N 2285 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12144 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 7.68, per 1000 atoms: 0.63 Number of scatterers: 12144 At special positions: 0 Unit cell: (123.201, 98.415, 114.453, 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 12 16.00 P 288 15.00 O 2845 8.00 N 2285 7.00 C 6714 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: 2.94 Conformation dependent library (CDL) restraints added in 993.0 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 75.5% alpha, 3.0% beta 141 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.435A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.755A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.509A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.461A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.531A pdb=" N THR K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 26 removed outlier: 3.793A pdb=" N GLU L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.532A pdb=" N THR M 10 " --> pdb=" O VAL M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.824A pdb=" N VAL N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.708A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.949A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.477A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 436 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 3.53 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: 2690 1.33 - 1.45: 3999 1.45 - 1.57: 5655 1.57 - 1.69: 576 1.69 - 1.81: 22 Bond restraints: 12942 Sorted by residual: bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.31e+00 bond pdb=" C4' DG J 2 " pdb=" C3' DG J 2 " ideal model delta sigma weight residual 1.523 1.503 0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 9.22e-01 bond pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.87e-01 bond pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.08e-02 8.57e+03 8.82e-01 ... (remaining 12937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 18051 1.42 - 2.83: 619 2.83 - 4.25: 44 4.25 - 5.66: 11 5.66 - 7.08: 3 Bond angle restraints: 18728 Sorted by residual: angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 119.78 -7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" CB GLU D 76 " pdb=" CG GLU D 76 " pdb=" CD GLU D 76 " ideal model delta sigma weight residual 112.60 116.44 -3.84 1.70e+00 3.46e-01 5.11e+00 angle pdb=" C GLY C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.10e+00 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 5014 25.88 - 51.77: 1577 51.77 - 77.65: 440 77.65 - 103.54: 6 103.54 - 129.42: 1 Dihedral angle restraints: 7038 sinusoidal: 4732 harmonic: 2306 Sorted by residual: dihedral pdb=" C4' DC J -38 " pdb=" C3' DC J -38 " pdb=" O3' DC J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 90.58 129.42 1 3.50e+01 8.16e-04 1.28e+01 dihedral pdb=" CA ARG M 7 " pdb=" CB ARG M 7 " pdb=" CG ARG M 7 " pdb=" CD ARG M 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.40 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG K 7 " pdb=" CB ARG K 7 " pdb=" CG ARG K 7 " pdb=" CD ARG K 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.38 59.38 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1463 0.030 - 0.060: 515 0.060 - 0.089: 115 0.089 - 0.119: 37 0.119 - 0.149: 11 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2138 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.023 2.00e-02 2.50e+03 9.23e-03 2.56e+00 pdb=" N9 DG I -35 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 17 " 0.020 2.00e-02 2.50e+03 9.30e-03 2.38e+00 pdb=" N9 DA J 17 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 17 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 17 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA J 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA J 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 17 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA J 17 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -49 " -0.018 2.00e-02 2.50e+03 8.66e-03 2.25e+00 pdb=" N9 DG J -49 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J -49 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -49 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J -49 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG J -49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG J -49 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG J -49 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG J -49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 590 2.70 - 3.25: 11214 3.25 - 3.80: 23934 3.80 - 4.35: 28428 4.35 - 4.90: 41259 Nonbonded interactions: 105425 Sorted by model distance: nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.164 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.165 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU G 64 " pdb=" NH1 ARG M 7 " model vdw 2.196 3.120 ... (remaining 105420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 36 through 124) selection = (chain 'H' and resid 36 through 124) } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 0.690 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 0.051 12942 Z= 0.221 Angle : 0.580 7.078 18728 Z= 0.349 Chirality : 0.034 0.149 2141 Planarity : 0.003 0.030 1371 Dihedral : 28.272 129.423 5546 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.32 % Allowed : 19.24 % Favored : 80.44 % 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: 2.60 (0.31), residues: 772 helix: 2.75 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.016 0.002 PHE F 100 TYR 0.018 0.001 TYR G 50 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.10853 ( 796) hydrogen bonds : angle 3.81554 ( 2004) covalent geometry : bond 0.00491 (12942) covalent geometry : angle 0.57990 (18728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.966 Fit side-chains REVERT: B 59 LYS cc_start: 0.9159 (tttm) cc_final: 0.8804 (tppp) REVERT: B 63 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 92 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 46 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8668 (mmmt) REVERT: H 71 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7976 (mm-30) outliers start: 2 outliers final: 5 residues processed: 224 average time/residue: 1.3841 time to fit residues: 331.9192 Evaluate side-chains 211 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 74 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 104 GLN C 112 GLN F 93 GLN G 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.036943 restraints weight = 42945.942| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.85 r_work: 0.2418 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12942 Z= 0.182 Angle : 0.553 5.609 18728 Z= 0.333 Chirality : 0.033 0.150 2141 Planarity : 0.004 0.036 1371 Dihedral : 30.812 129.768 4061 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.42 % Allowed : 25.24 % Favored : 73.34 % 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: 2.77 (0.31), residues: 772 helix: 2.80 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.55 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.014 0.002 PHE F 100 TYR 0.015 0.001 TYR G 57 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 796) hydrogen bonds : angle 3.03778 ( 2004) covalent geometry : bond 0.00399 (12942) covalent geometry : angle 0.55255 (18728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.954 Fit side-chains REVERT: A 59 GLU cc_start: 0.9014 (pm20) cc_final: 0.8784 (pm20) REVERT: B 59 LYS cc_start: 0.9239 (tttm) cc_final: 0.8904 (tppp) REVERT: B 63 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8917 (mt-10) REVERT: C 56 GLU cc_start: 0.9275 (tt0) cc_final: 0.9013 (tt0) REVERT: C 90 ASP cc_start: 0.8446 (t70) cc_final: 0.7958 (t0) REVERT: C 92 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8704 (mt-10) REVERT: D 93 GLU cc_start: 0.9201 (mp0) cc_final: 0.8873 (mm-30) REVERT: D 105 GLU cc_start: 0.8605 (tp30) cc_final: 0.8074 (tp30) REVERT: E 59 GLU cc_start: 0.8917 (pm20) cc_final: 0.8707 (pm20) REVERT: G 39 TYR cc_start: 0.9361 (m-80) cc_final: 0.9058 (m-80) REVERT: G 41 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8177 (tm-30) REVERT: G 64 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9019 (tm-30) REVERT: H 46 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8932 (mmmt) REVERT: H 68 ASP cc_start: 0.9563 (t0) cc_final: 0.9308 (t0) REVERT: H 71 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9078 (mm-30) REVERT: H 105 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8303 (tm-30) outliers start: 9 outliers final: 6 residues processed: 240 average time/residue: 1.3347 time to fit residues: 344.1612 Evaluate side-chains 215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN E 113 HIS G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036188 restraints weight = 44760.725| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.86 r_work: 0.2395 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12942 Z= 0.244 Angle : 0.571 6.559 18728 Z= 0.342 Chirality : 0.034 0.144 2141 Planarity : 0.004 0.036 1371 Dihedral : 30.876 130.231 4055 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 26.66 % Favored : 70.66 % 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: 2.90 (0.31), residues: 772 helix: 2.90 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.48 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.016 0.002 PHE F 100 TYR 0.014 0.001 TYR G 57 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 796) hydrogen bonds : angle 3.04680 ( 2004) covalent geometry : bond 0.00543 (12942) covalent geometry : angle 0.57116 (18728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.913 Fit side-chains REVERT: A 59 GLU cc_start: 0.8949 (pm20) cc_final: 0.8717 (pm20) REVERT: B 59 LYS cc_start: 0.9319 (tttm) cc_final: 0.9030 (tppp) REVERT: B 63 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8983 (mt-10) REVERT: C 56 GLU cc_start: 0.9280 (tt0) cc_final: 0.8948 (tt0) REVERT: C 90 ASP cc_start: 0.8634 (t70) cc_final: 0.8287 (t0) REVERT: C 92 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8732 (mt-10) REVERT: D 68 ASP cc_start: 0.9454 (t0) cc_final: 0.9239 (t0) REVERT: D 86 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8460 (tpp80) REVERT: D 93 GLU cc_start: 0.9231 (mp0) cc_final: 0.8979 (mp0) REVERT: E 59 GLU cc_start: 0.8970 (pm20) cc_final: 0.8691 (pm20) REVERT: G 41 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8170 (tm-30) REVERT: G 64 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9076 (tm-30) REVERT: G 90 ASP cc_start: 0.9054 (t0) cc_final: 0.8848 (t0) REVERT: H 34 LYS cc_start: 0.9052 (mppt) cc_final: 0.8769 (mmpt) REVERT: H 46 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8974 (mmmt) REVERT: H 68 ASP cc_start: 0.9548 (t0) cc_final: 0.9272 (t0) REVERT: H 71 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9106 (mm-30) REVERT: H 105 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8415 (tm-30) outliers start: 17 outliers final: 10 residues processed: 217 average time/residue: 1.5076 time to fit residues: 350.3755 Evaluate side-chains 210 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 101 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.036581 restraints weight = 44326.237| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 2.84 r_work: 0.2410 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12942 Z= 0.208 Angle : 0.564 7.555 18728 Z= 0.337 Chirality : 0.033 0.153 2141 Planarity : 0.004 0.037 1371 Dihedral : 30.834 130.119 4055 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.94 % Allowed : 26.34 % Favored : 69.72 % 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: 2.97 (0.31), residues: 772 helix: 2.95 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE F 100 TYR 0.016 0.002 TYR G 57 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 796) hydrogen bonds : angle 2.95577 ( 2004) covalent geometry : bond 0.00462 (12942) covalent geometry : angle 0.56368 (18728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.905 Fit side-chains REVERT: A 59 GLU cc_start: 0.8928 (pm20) cc_final: 0.8593 (pm20) REVERT: B 59 LYS cc_start: 0.9309 (tttm) cc_final: 0.8964 (tppp) REVERT: B 63 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8875 (mt-10) REVERT: C 56 GLU cc_start: 0.9274 (tt0) cc_final: 0.8900 (tt0) REVERT: C 64 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8865 (tm-30) REVERT: C 90 ASP cc_start: 0.8636 (t70) cc_final: 0.8139 (t0) REVERT: C 92 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8511 (mt-10) REVERT: D 68 ASP cc_start: 0.9436 (t0) cc_final: 0.9175 (t0) REVERT: D 86 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8437 (tpp80) REVERT: D 93 GLU cc_start: 0.9225 (mp0) cc_final: 0.8930 (mp0) REVERT: E 59 GLU cc_start: 0.8967 (pm20) cc_final: 0.8665 (pm20) REVERT: G 41 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8247 (tm-30) REVERT: G 64 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9048 (tm-30) REVERT: G 90 ASP cc_start: 0.9001 (t0) cc_final: 0.8776 (t0) REVERT: H 34 LYS cc_start: 0.9079 (mppt) cc_final: 0.8681 (mmpt) REVERT: H 46 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8960 (mmmt) REVERT: H 68 ASP cc_start: 0.9545 (t0) cc_final: 0.9251 (t0) REVERT: H 71 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9103 (mm-30) REVERT: H 105 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8274 (tm-30) outliers start: 25 outliers final: 13 residues processed: 226 average time/residue: 1.3448 time to fit residues: 326.5563 Evaluate side-chains 218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN D 95 GLN G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.036674 restraints weight = 44206.147| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.85 r_work: 0.2417 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12942 Z= 0.209 Angle : 0.570 8.068 18728 Z= 0.338 Chirality : 0.034 0.144 2141 Planarity : 0.004 0.038 1371 Dihedral : 30.819 130.112 4055 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.79 % Allowed : 26.66 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.01 (0.31), residues: 772 helix: 2.98 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE F 100 TYR 0.020 0.001 TYR G 50 ARG 0.007 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 796) hydrogen bonds : angle 2.92113 ( 2004) covalent geometry : bond 0.00465 (12942) covalent geometry : angle 0.56986 (18728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.918 Fit side-chains REVERT: A 59 GLU cc_start: 0.9023 (pm20) cc_final: 0.8717 (pm20) REVERT: B 59 LYS cc_start: 0.9317 (tttm) cc_final: 0.8980 (tppp) REVERT: B 63 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8889 (mt-10) REVERT: C 56 GLU cc_start: 0.9272 (tt0) cc_final: 0.8863 (tt0) REVERT: C 90 ASP cc_start: 0.8587 (t70) cc_final: 0.8313 (t0) REVERT: C 92 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8739 (mt-10) REVERT: D 68 ASP cc_start: 0.9419 (t0) cc_final: 0.9196 (t0) REVERT: D 86 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8428 (tpp80) REVERT: D 93 GLU cc_start: 0.9216 (mp0) cc_final: 0.8902 (mp0) REVERT: E 59 GLU cc_start: 0.8957 (pm20) cc_final: 0.8654 (pm20) REVERT: G 41 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 64 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9062 (tm-30) REVERT: G 90 ASP cc_start: 0.9005 (t0) cc_final: 0.8770 (t0) REVERT: H 34 LYS cc_start: 0.9085 (mppt) cc_final: 0.8721 (mmpt) REVERT: H 46 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8953 (mmmt) REVERT: H 68 ASP cc_start: 0.9542 (t0) cc_final: 0.9244 (t0) REVERT: H 71 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9102 (mm-30) REVERT: H 105 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8242 (tm-30) outliers start: 24 outliers final: 12 residues processed: 225 average time/residue: 1.2771 time to fit residues: 309.4420 Evaluate side-chains 219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036182 restraints weight = 45169.150| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.86 r_work: 0.2396 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12942 Z= 0.242 Angle : 0.586 10.188 18728 Z= 0.346 Chirality : 0.035 0.159 2141 Planarity : 0.004 0.038 1371 Dihedral : 30.896 130.045 4055 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.10 % Allowed : 27.44 % Favored : 68.45 % 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: 3.06 (0.31), residues: 772 helix: 3.01 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE F 100 TYR 0.021 0.002 TYR G 50 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 796) hydrogen bonds : angle 2.97928 ( 2004) covalent geometry : bond 0.00542 (12942) covalent geometry : angle 0.58639 (18728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9070 (pm20) cc_final: 0.8771 (pm20) REVERT: A 105 GLU cc_start: 0.9212 (tt0) cc_final: 0.8989 (tp30) REVERT: B 59 LYS cc_start: 0.9332 (tttm) cc_final: 0.9040 (tppp) REVERT: B 63 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8986 (mt-10) REVERT: C 56 GLU cc_start: 0.9291 (tt0) cc_final: 0.8978 (tt0) REVERT: C 64 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8970 (tm-30) REVERT: C 90 ASP cc_start: 0.8682 (t70) cc_final: 0.8176 (t0) REVERT: C 92 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8530 (mt-10) REVERT: D 68 ASP cc_start: 0.9419 (t0) cc_final: 0.9185 (t0) REVERT: D 86 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8463 (tpp80) REVERT: D 93 GLU cc_start: 0.9240 (mp0) cc_final: 0.8914 (mp0) REVERT: E 59 GLU cc_start: 0.8961 (pm20) cc_final: 0.8641 (pm20) REVERT: G 41 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 64 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9073 (tm-30) REVERT: G 90 ASP cc_start: 0.9069 (t0) cc_final: 0.8813 (t0) REVERT: H 34 LYS cc_start: 0.9117 (mppt) cc_final: 0.8715 (mmpt) REVERT: H 46 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8945 (mmmt) REVERT: H 68 ASP cc_start: 0.9541 (t0) cc_final: 0.9235 (t0) REVERT: H 71 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9100 (mm-30) REVERT: H 105 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8252 (tm-30) outliers start: 26 outliers final: 14 residues processed: 224 average time/residue: 1.3846 time to fit residues: 332.6616 Evaluate side-chains 222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.038924 restraints weight = 43433.594| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.87 r_work: 0.2480 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12942 Z= 0.147 Angle : 0.569 11.592 18728 Z= 0.334 Chirality : 0.032 0.150 2141 Planarity : 0.004 0.041 1371 Dihedral : 30.568 129.590 4055 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.37 % Allowed : 29.18 % Favored : 68.45 % 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: 3.09 (0.30), residues: 772 helix: 3.04 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.48 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE F 100 TYR 0.019 0.001 TYR G 50 ARG 0.008 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 796) hydrogen bonds : angle 2.71090 ( 2004) covalent geometry : bond 0.00317 (12942) covalent geometry : angle 0.56930 (18728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.903 Fit side-chains REVERT: A 59 GLU cc_start: 0.8981 (pm20) cc_final: 0.8705 (pm20) REVERT: B 59 LYS cc_start: 0.9223 (tttm) cc_final: 0.8974 (tppp) REVERT: C 56 GLU cc_start: 0.9275 (tt0) cc_final: 0.8864 (tt0) REVERT: C 90 ASP cc_start: 0.8576 (t70) cc_final: 0.7913 (t0) REVERT: C 92 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8720 (mp0) REVERT: D 68 ASP cc_start: 0.9383 (t0) cc_final: 0.9165 (t0) REVERT: D 93 GLU cc_start: 0.9186 (mp0) cc_final: 0.8828 (mp0) REVERT: D 105 GLU cc_start: 0.8438 (tp30) cc_final: 0.7585 (tp30) REVERT: E 59 GLU cc_start: 0.8824 (pm20) cc_final: 0.8471 (pm20) REVERT: E 107 THR cc_start: 0.9765 (m) cc_final: 0.9491 (p) REVERT: G 64 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9036 (tm-30) REVERT: G 90 ASP cc_start: 0.8990 (t0) cc_final: 0.8689 (t0) REVERT: H 34 LYS cc_start: 0.9099 (mppt) cc_final: 0.8685 (mmpt) REVERT: H 46 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8904 (mmmt) REVERT: H 68 ASP cc_start: 0.9541 (t0) cc_final: 0.9262 (t0) REVERT: H 71 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9100 (mm-30) REVERT: H 105 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8008 (tm-30) outliers start: 15 outliers final: 6 residues processed: 238 average time/residue: 1.3399 time to fit residues: 342.6043 Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037883 restraints weight = 44713.709| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.84 r_work: 0.2458 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12942 Z= 0.181 Angle : 0.581 11.303 18728 Z= 0.339 Chirality : 0.033 0.159 2141 Planarity : 0.004 0.043 1371 Dihedral : 30.678 129.756 4055 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.21 % Allowed : 31.39 % Favored : 66.40 % 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: 3.19 (0.30), residues: 772 helix: 3.11 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE F 100 TYR 0.021 0.002 TYR G 50 ARG 0.010 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 796) hydrogen bonds : angle 2.81181 ( 2004) covalent geometry : bond 0.00402 (12942) covalent geometry : angle 0.58146 (18728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9076 (pm20) cc_final: 0.8848 (pm20) REVERT: B 59 LYS cc_start: 0.9256 (tttm) cc_final: 0.9055 (tppp) REVERT: C 56 GLU cc_start: 0.9272 (tt0) cc_final: 0.8850 (tt0) REVERT: C 90 ASP cc_start: 0.8457 (t70) cc_final: 0.8248 (t0) REVERT: C 92 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8499 (mt-10) REVERT: D 68 ASP cc_start: 0.9390 (t0) cc_final: 0.9163 (t0) REVERT: D 93 GLU cc_start: 0.9183 (mp0) cc_final: 0.8843 (mp0) REVERT: E 59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8506 (pm20) REVERT: E 107 THR cc_start: 0.9739 (m) cc_final: 0.9507 (p) REVERT: G 64 GLU cc_start: 0.9396 (tt0) cc_final: 0.9066 (tm-30) REVERT: H 34 LYS cc_start: 0.9131 (mppt) cc_final: 0.8695 (mmpt) REVERT: H 46 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8888 (mmmt) REVERT: H 68 ASP cc_start: 0.9526 (t0) cc_final: 0.9233 (t0) REVERT: H 71 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9100 (mm-30) REVERT: H 105 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8027 (tm-30) outliers start: 14 outliers final: 8 residues processed: 228 average time/residue: 1.3457 time to fit residues: 330.2737 Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038873 restraints weight = 43174.591| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.86 r_work: 0.2478 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12942 Z= 0.159 Angle : 0.600 11.836 18728 Z= 0.345 Chirality : 0.032 0.160 2141 Planarity : 0.004 0.042 1371 Dihedral : 30.580 129.350 4055 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.10 % Allowed : 32.33 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.08 (0.30), residues: 772 helix: 3.02 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.38 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 100 TYR 0.020 0.001 TYR G 50 ARG 0.011 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 796) hydrogen bonds : angle 2.78762 ( 2004) covalent geometry : bond 0.00351 (12942) covalent geometry : angle 0.59987 (18728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9065 (pm20) cc_final: 0.8797 (pm20) REVERT: C 56 GLU cc_start: 0.9274 (tt0) cc_final: 0.8839 (tt0) REVERT: C 90 ASP cc_start: 0.8567 (t70) cc_final: 0.7934 (t0) REVERT: C 92 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8730 (mp0) REVERT: D 68 ASP cc_start: 0.9391 (t0) cc_final: 0.9171 (t0) REVERT: D 93 GLU cc_start: 0.9195 (mp0) cc_final: 0.8846 (mp0) REVERT: D 105 GLU cc_start: 0.8487 (tp30) cc_final: 0.7672 (tp30) REVERT: E 59 GLU cc_start: 0.8803 (pm20) cc_final: 0.8457 (pm20) REVERT: E 107 THR cc_start: 0.9745 (m) cc_final: 0.9516 (p) REVERT: G 90 ASP cc_start: 0.9031 (t0) cc_final: 0.8735 (t0) REVERT: H 34 LYS cc_start: 0.9099 (mppt) cc_final: 0.8661 (mmpt) REVERT: H 46 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8895 (mmmt) REVERT: H 68 ASP cc_start: 0.9550 (t0) cc_final: 0.9244 (t0) REVERT: H 71 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9099 (mm-30) REVERT: H 105 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8118 (tm-30) outliers start: 7 outliers final: 8 residues processed: 221 average time/residue: 1.5949 time to fit residues: 380.0947 Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 99 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037224 restraints weight = 44575.022| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.85 r_work: 0.2436 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12942 Z= 0.216 Angle : 0.616 12.104 18728 Z= 0.354 Chirality : 0.034 0.168 2141 Planarity : 0.004 0.052 1371 Dihedral : 30.703 129.357 4055 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.26 % Allowed : 32.65 % Favored : 66.09 % 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: 3.12 (0.30), residues: 772 helix: 3.06 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE F 100 TYR 0.024 0.002 TYR G 50 ARG 0.011 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 796) hydrogen bonds : angle 2.94971 ( 2004) covalent geometry : bond 0.00484 (12942) covalent geometry : angle 0.61608 (18728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9113 (pm20) cc_final: 0.8818 (pm20) REVERT: A 76 GLN cc_start: 0.9126 (pt0) cc_final: 0.8680 (pp30) REVERT: C 56 GLU cc_start: 0.9284 (tt0) cc_final: 0.8837 (tt0) REVERT: C 90 ASP cc_start: 0.8487 (t70) cc_final: 0.8248 (t0) REVERT: C 92 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8464 (mt-10) REVERT: D 68 ASP cc_start: 0.9405 (t0) cc_final: 0.9176 (t0) REVERT: D 105 GLU cc_start: 0.8613 (tp30) cc_final: 0.8229 (tp30) REVERT: E 59 GLU cc_start: 0.8895 (pm20) cc_final: 0.8545 (pm20) REVERT: G 64 GLU cc_start: 0.9419 (tt0) cc_final: 0.9067 (tm-30) REVERT: G 90 ASP cc_start: 0.9067 (t0) cc_final: 0.8823 (t0) REVERT: H 34 LYS cc_start: 0.9109 (mppt) cc_final: 0.8650 (mmpt) REVERT: H 46 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8898 (mmmt) REVERT: H 68 ASP cc_start: 0.9539 (t0) cc_final: 0.9234 (t0) REVERT: H 71 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9082 (mm-30) REVERT: H 105 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8253 (tm-30) outliers start: 8 outliers final: 8 residues processed: 212 average time/residue: 1.3695 time to fit residues: 312.0238 Evaluate side-chains 215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.058089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.037420 restraints weight = 44359.025| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.87 r_work: 0.2446 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12942 Z= 0.197 Angle : 0.620 11.869 18728 Z= 0.356 Chirality : 0.033 0.164 2141 Planarity : 0.004 0.048 1371 Dihedral : 30.653 128.988 4055 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.95 % Allowed : 32.97 % Favored : 66.09 % 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: 3.05 (0.30), residues: 772 helix: 3.01 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE F 100 TYR 0.025 0.002 TYR G 50 ARG 0.011 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 796) hydrogen bonds : angle 2.90532 ( 2004) covalent geometry : bond 0.00442 (12942) covalent geometry : angle 0.62036 (18728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8990.05 seconds wall clock time: 155 minutes 33.58 seconds (9333.58 seconds total)