Starting phenix.real_space_refine on Wed Jun 11 05:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu4_48619/06_2025/9mu4_48619.cif" } resolution = 3.29 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= 0.006 sd= 0.039 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 328 5.49 5 S 14 5.16 5 C 7024 2.51 5 N 2384 2.21 5 O 3044 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-5710/modules/chem_data/mon_lib" Total number of atoms: 12794 Number of models: 1 Model: "" Number of chains: 10 Chain: "c" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "d" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "e" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "T" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3344 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain breaks: 2 Chain: "N" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3380 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Time building chain proxies: 8.21, per 1000 atoms: 0.64 Number of scatterers: 12794 At special positions: 0 Unit cell: (118.841, 80.766, 159.224, 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 14 16.00 P 328 15.00 O 3044 8.00 N 2384 7.00 C 7024 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: 3.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 70.8% alpha, 3.1% beta 163 base pairs and 298 stacking pairs defined. Time for finding SS restraints: 6.46 Creating SS restraints... Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.620A pdb=" N ILE c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.525A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.797A pdb=" N ILE g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.412A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 removed outlier: 3.576A pdb=" N LEU g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP g 90 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'd' and resid 35 through 47 Processing helix chain 'd' and resid 53 through 82 removed outlier: 3.668A pdb=" N ASN d 82 " --> pdb=" O LEU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 100 removed outlier: 3.746A pdb=" N ILE d 92 " --> pdb=" O THR d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 122 removed outlier: 3.803A pdb=" N LYS d 106 " --> pdb=" O GLY d 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 47 Processing helix chain 'h' and resid 53 through 82 removed outlier: 3.566A pdb=" N ASN h 82 " --> pdb=" O LEU h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 100 removed outlier: 3.598A pdb=" N ILE h 92 " --> pdb=" O THR h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 123 removed outlier: 3.906A pdb=" N LYS h 106 " --> pdb=" O GLY h 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 64 through 80 removed outlier: 3.545A pdb=" N PHE a 68 " --> pdb=" O ARG a 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 115 Processing helix chain 'a' and resid 121 through 132 removed outlier: 3.507A pdb=" N ILE a 125 " --> pdb=" O MET a 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 56 Processing helix chain 'e' and resid 64 through 80 removed outlier: 3.526A pdb=" N PHE e 68 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE e 79 " --> pdb=" O ILE e 75 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS e 80 " --> pdb=" O ALA e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 115 Processing helix chain 'e' and resid 121 through 132 removed outlier: 3.686A pdb=" N ILE e 125 " --> pdb=" O MET e 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 30 Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.966A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA b 77 " --> pdb=" O TYR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 94 removed outlier: 3.713A pdb=" N VAL b 87 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 30 removed outlier: 4.004A pdb=" N GLN f 28 " --> pdb=" O ASP f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 43 Processing helix chain 'f' and resid 50 through 77 removed outlier: 3.915A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG f 68 " --> pdb=" O GLU f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 94 removed outlier: 3.604A pdb=" N VAL f 87 " --> pdb=" O THR f 83 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN f 94 " --> pdb=" O ALA f 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG c 42 " --> pdb=" O ILE d 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.549A pdb=" N ARG g 42 " --> pdb=" O ILE h 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'g' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85 removed outlier: 7.153A pdb=" N ARG a 84 " --> pdb=" O VAL b 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'e' and resid 84 through 85 removed outlier: 6.973A pdb=" N ARG e 84 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'e' and resid 119 through 120 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 812 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 298 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.99 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: 2495 1.33 - 1.46: 4769 1.46 - 1.58: 5748 1.58 - 1.70: 652 1.70 - 1.82: 26 Bond restraints: 13690 Sorted by residual: bond pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.55e+00 bond pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " ideal model delta sigma weight residual 1.422 1.493 -0.071 3.00e-02 1.11e+03 5.61e+00 bond pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.27e+00 bond pdb=" C3' DT T 43 " pdb=" O3' DT T 43 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.90e+00 bond pdb=" C3' DG T -30 " pdb=" O3' DG T -30 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.67e+00 ... (remaining 13685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 19471 2.34 - 4.67: 387 4.67 - 7.01: 31 7.01 - 9.35: 7 9.35 - 11.68: 4 Bond angle restraints: 19900 Sorted by residual: angle pdb=" C GLY c 37 " pdb=" N ASN c 38 " pdb=" CA ASN c 38 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C GLY g 37 " pdb=" N ASN g 38 " pdb=" CA ASN g 38 " ideal model delta sigma weight residual 122.46 129.39 -6.93 1.41e+00 5.03e-01 2.41e+01 angle pdb=" CB MET b 85 " pdb=" CG MET b 85 " pdb=" SD MET b 85 " ideal model delta sigma weight residual 112.70 124.38 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA GLU f 75 " pdb=" CB GLU f 75 " pdb=" CG GLU f 75 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " pdb=" P DT N 76 " ideal model delta sigma weight residual 120.20 125.67 -5.47 1.50e+00 4.44e-01 1.33e+01 ... (remaining 19895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 5730 34.50 - 69.00: 1666 69.00 - 103.51: 22 103.51 - 138.01: 8 138.01 - 172.51: 2 Dihedral angle restraints: 7428 sinusoidal: 5192 harmonic: 2236 Sorted by residual: dihedral pdb=" CA ILE b 30 " pdb=" C ILE b 30 " pdb=" N THR b 31 " pdb=" CA THR b 31 " ideal model delta harmonic sigma weight residual 180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C4' DA N 75 " pdb=" C3' DA N 75 " pdb=" O3' DA N 75 " pdb=" P DT N 76 " ideal model delta sinusoidal sigma weight residual 220.00 47.49 172.51 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT N -17 " pdb=" C3' DT N -17 " pdb=" O3' DT N -17 " pdb=" P DT N -16 " ideal model delta sinusoidal sigma weight residual 220.00 50.33 169.67 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2085 0.081 - 0.162: 168 0.162 - 0.243: 8 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CG LEU g 63 " pdb=" CB LEU g 63 " pdb=" CD1 LEU g 63 " pdb=" CD2 LEU g 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE h 52 " pdb=" CA ILE h 52 " pdb=" CG1 ILE h 52 " pdb=" CG2 ILE h 52 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE d 52 " pdb=" CA ILE d 52 " pdb=" CG1 ILE d 52 " pdb=" CG2 ILE d 52 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2261 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE g 79 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO g 80 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO g 80 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO g 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET e 121 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO e 122 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO e 122 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO e 122 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 119 " -0.010 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR d 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR d 119 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR d 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR d 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR d 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR d 119 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR d 119 " 0.003 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2891 2.82 - 3.34: 10658 3.34 - 3.86: 25488 3.86 - 4.38: 29416 4.38 - 4.90: 40972 Nonbonded interactions: 109425 Sorted by model distance: nonbonded pdb=" O TYR g 39 " pdb=" OG SER h 76 " model vdw 2.302 3.040 nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 76 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG c 32 " pdb=" OP1 DA T -44 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG c 71 " pdb=" OG1 THR d 50 " model vdw 2.360 3.120 nonbonded pdb=" NE2 GLN g 24 " pdb=" OE1 GLN h 45 " model vdw 2.378 3.120 ... (remaining 109420 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.230 Find NCS groups from input model: 0.250 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.006 0.077 13690 Z= 0.263 Angle : 0.838 11.683 19900 Z= 0.481 Chirality : 0.047 0.405 2264 Planarity : 0.007 0.072 1388 Dihedral : 28.803 172.510 5984 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -1.86 (0.25), residues: 754 helix: -0.72 (0.18), residues: 536 sheet: None (None), residues: 0 loop : -2.25 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS c 82 PHE 0.019 0.002 PHE c 25 TYR 0.039 0.003 TYR d 119 ARG 0.011 0.001 ARG d 77 Details of bonding type rmsd hydrogen bonds : bond 0.09654 ( 794) hydrogen bonds : angle 3.89937 ( 1964) covalent geometry : bond 0.00612 (13690) covalent geometry : angle 0.83771 (19900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.805 Fit side-chains REVERT: g 90 ASP cc_start: 0.8303 (t0) cc_final: 0.8009 (t0) REVERT: g 92 GLU cc_start: 0.8709 (mp0) cc_final: 0.8430 (mp0) REVERT: g 100 VAL cc_start: 0.9141 (t) cc_final: 0.8491 (t) REVERT: d 32 LYS cc_start: 0.8972 (tppt) cc_final: 0.8683 (mmmm) REVERT: h 81 TYR cc_start: 0.8667 (m-10) cc_final: 0.8439 (m-10) REVERT: h 83 LYS cc_start: 0.9350 (mptt) cc_final: 0.9077 (mttp) REVERT: h 103 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7898 (mm-30) REVERT: a 60 GLU cc_start: 0.8588 (pm20) cc_final: 0.8352 (pm20) REVERT: a 74 GLU cc_start: 0.8485 (tt0) cc_final: 0.8213 (tt0) REVERT: a 82 ASP cc_start: 0.8563 (t0) cc_final: 0.8225 (t0) REVERT: a 91 MET cc_start: 0.8948 (mpp) cc_final: 0.8579 (mmm) REVERT: a 94 GLN cc_start: 0.8962 (tt0) cc_final: 0.8638 (tt0) REVERT: a 108 THR cc_start: 0.9347 (m) cc_final: 0.9136 (t) REVERT: b 26 ASN cc_start: 0.9113 (m110) cc_final: 0.8815 (m110) REVERT: b 68 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8241 (ttm170) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3122 time to fit residues: 73.3327 Evaluate side-chains 145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 24 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 = 0.3929 r_free = 0.3929 target = 0.094957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066005 restraints weight = 40101.377| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.96 r_work: 0.3108 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 0.044 13690 Z= 0.202 Angle : 0.598 5.589 19900 Z= 0.361 Chirality : 0.035 0.158 2264 Planarity : 0.005 0.052 1388 Dihedral : 31.610 172.930 4484 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 8.44 % Favored : 89.97 % 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: 0.61 (0.29), residues: 754 helix: 1.29 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.89 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 76 PHE 0.007 0.001 PHE c 25 TYR 0.027 0.002 TYR b 99 ARG 0.003 0.000 ARG c 35 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 794) hydrogen bonds : angle 2.71390 ( 1964) covalent geometry : bond 0.00452 (13690) covalent geometry : angle 0.59816 (19900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.904 Fit side-chains REVERT: c 19 ASN cc_start: 0.8961 (t0) cc_final: 0.8728 (t0) REVERT: d 32 LYS cc_start: 0.8803 (tppt) cc_final: 0.8500 (mmmm) REVERT: h 49 ASP cc_start: 0.8608 (m-30) cc_final: 0.8186 (t0) REVERT: h 81 TYR cc_start: 0.8721 (m-10) cc_final: 0.8332 (m-10) REVERT: h 83 LYS cc_start: 0.9297 (mptt) cc_final: 0.9040 (mttp) REVERT: a 57 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8703 (ttmt) REVERT: a 60 GLU cc_start: 0.8715 (pm20) cc_final: 0.8484 (pm20) REVERT: a 74 GLU cc_start: 0.8399 (tt0) cc_final: 0.8108 (tt0) REVERT: a 82 ASP cc_start: 0.8561 (t0) cc_final: 0.8258 (t0) REVERT: a 91 MET cc_start: 0.8785 (mpp) cc_final: 0.8460 (mmm) REVERT: e 91 MET cc_start: 0.8850 (mmt) cc_final: 0.8631 (mmt) REVERT: b 26 ASN cc_start: 0.8974 (m110) cc_final: 0.8619 (m110) REVERT: b 68 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8398 (ttm170) outliers start: 10 outliers final: 6 residues processed: 163 average time/residue: 0.3024 time to fit residues: 66.5116 Evaluate side-chains 147 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 83 LYS Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 24 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 = 0.3928 r_free = 0.3928 target = 0.095011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065905 restraints weight = 39950.027| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.79 r_work: 0.3111 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13690 Z= 0.192 Angle : 0.583 5.513 19900 Z= 0.352 Chirality : 0.034 0.145 2264 Planarity : 0.004 0.046 1388 Dihedral : 31.607 173.422 4484 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.43 % Allowed : 11.46 % Favored : 87.10 % 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: 1.45 (0.30), residues: 754 helix: 1.96 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.69 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS f 76 PHE 0.006 0.001 PHE g 25 TYR 0.017 0.002 TYR b 99 ARG 0.004 0.000 ARG c 35 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 794) hydrogen bonds : angle 2.60865 ( 1964) covalent geometry : bond 0.00427 (13690) covalent geometry : angle 0.58299 (19900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.928 Fit side-chains REVERT: c 19 ASN cc_start: 0.8965 (t0) cc_final: 0.8670 (t0) REVERT: d 32 LYS cc_start: 0.8777 (tppt) cc_final: 0.8467 (mmmm) REVERT: h 49 ASP cc_start: 0.8609 (m-30) cc_final: 0.8194 (t0) REVERT: h 81 TYR cc_start: 0.8743 (m-10) cc_final: 0.8347 (m-10) REVERT: h 83 LYS cc_start: 0.9296 (mptt) cc_final: 0.9033 (mttp) REVERT: a 57 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8730 (ttmt) REVERT: a 60 GLU cc_start: 0.8716 (pm20) cc_final: 0.8454 (pm20) REVERT: a 82 ASP cc_start: 0.8563 (t0) cc_final: 0.8264 (t0) REVERT: a 88 SER cc_start: 0.9065 (p) cc_final: 0.8734 (t) REVERT: a 91 MET cc_start: 0.8841 (mpp) cc_final: 0.8494 (mmm) REVERT: e 91 MET cc_start: 0.8799 (mmt) cc_final: 0.8518 (mmt) REVERT: b 68 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8396 (ttm170) REVERT: b 89 TYR cc_start: 0.8693 (m-10) cc_final: 0.8254 (m-80) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.3127 time to fit residues: 63.0227 Evaluate side-chains 142 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 68 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 82 ASN a 94 GLN ** f 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.094855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065761 restraints weight = 39818.874| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.86 r_work: 0.3108 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13690 Z= 0.197 Angle : 0.580 5.479 19900 Z= 0.350 Chirality : 0.034 0.141 2264 Planarity : 0.004 0.043 1388 Dihedral : 31.654 174.872 4484 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.39 % Allowed : 12.58 % Favored : 85.03 % 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: 1.83 (0.31), residues: 754 helix: 2.23 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 76 PHE 0.009 0.001 PHE c 25 TYR 0.021 0.001 TYR d 81 ARG 0.004 0.000 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 794) hydrogen bonds : angle 2.55246 ( 1964) covalent geometry : bond 0.00440 (13690) covalent geometry : angle 0.58015 (19900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.885 Fit side-chains REVERT: c 19 ASN cc_start: 0.8975 (t0) cc_final: 0.8661 (t0) REVERT: c 63 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8871 (mt) REVERT: c 71 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7315 (mmt-90) REVERT: c 72 ASP cc_start: 0.8722 (t0) cc_final: 0.8092 (m-30) REVERT: d 32 LYS cc_start: 0.8756 (tppt) cc_final: 0.8452 (mmmm) REVERT: h 49 ASP cc_start: 0.8670 (m-30) cc_final: 0.8270 (t0) REVERT: h 77 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8663 (mtm-85) REVERT: h 81 TYR cc_start: 0.8818 (m-10) cc_final: 0.8445 (m-10) REVERT: h 83 LYS cc_start: 0.9280 (mptt) cc_final: 0.9013 (mttp) REVERT: a 57 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8773 (ttmt) REVERT: a 60 GLU cc_start: 0.8719 (pm20) cc_final: 0.8335 (pm20) REVERT: a 82 ASP cc_start: 0.8584 (t0) cc_final: 0.8290 (t0) REVERT: a 88 SER cc_start: 0.9075 (p) cc_final: 0.8770 (t) REVERT: b 26 ASN cc_start: 0.8904 (m110) cc_final: 0.8677 (m-40) REVERT: b 68 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8433 (ttm170) REVERT: b 89 TYR cc_start: 0.8531 (m-10) cc_final: 0.8199 (m-80) outliers start: 15 outliers final: 10 residues processed: 160 average time/residue: 0.2919 time to fit residues: 63.1321 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.0010 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.094719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065580 restraints weight = 39974.933| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.89 r_work: 0.3099 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13690 Z= 0.202 Angle : 0.585 5.518 19900 Z= 0.352 Chirality : 0.034 0.144 2264 Planarity : 0.004 0.043 1388 Dihedral : 31.699 177.155 4484 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.23 % Allowed : 12.74 % Favored : 85.03 % 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: 2.02 (0.31), residues: 754 helix: 2.33 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 76 PHE 0.010 0.001 PHE c 25 TYR 0.010 0.001 TYR c 57 ARG 0.004 0.000 ARG c 35 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 794) hydrogen bonds : angle 2.54530 ( 1964) covalent geometry : bond 0.00452 (13690) covalent geometry : angle 0.58495 (19900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8948 (t0) cc_final: 0.8605 (t0) REVERT: c 63 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8901 (mt) REVERT: c 71 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7336 (mtt90) REVERT: g 63 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9002 (mt) REVERT: d 32 LYS cc_start: 0.8779 (tppt) cc_final: 0.8469 (mmmm) REVERT: h 49 ASP cc_start: 0.8641 (m-30) cc_final: 0.8272 (t0) REVERT: h 77 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8624 (mtm-85) REVERT: h 81 TYR cc_start: 0.8889 (m-10) cc_final: 0.8483 (m-10) REVERT: h 83 LYS cc_start: 0.9291 (mptt) cc_final: 0.9024 (mttp) REVERT: a 57 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8784 (ttmt) REVERT: a 60 GLU cc_start: 0.8759 (pm20) cc_final: 0.8370 (pm20) REVERT: a 82 ASP cc_start: 0.8595 (t0) cc_final: 0.8279 (t0) REVERT: a 88 SER cc_start: 0.9062 (p) cc_final: 0.8768 (t) REVERT: a 98 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7615 (mt-10) outliers start: 14 outliers final: 9 residues processed: 158 average time/residue: 0.2968 time to fit residues: 63.6263 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3938 r_free = 0.3938 target = 0.095533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066403 restraints weight = 40384.478| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.79 r_work: 0.3122 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13690 Z= 0.176 Angle : 0.578 8.396 19900 Z= 0.347 Chirality : 0.034 0.142 2264 Planarity : 0.004 0.041 1388 Dihedral : 31.553 178.245 4484 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.23 % Allowed : 13.69 % Favored : 84.08 % 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: 2.17 (0.31), residues: 754 helix: 2.47 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS b 76 PHE 0.007 0.001 PHE c 25 TYR 0.009 0.001 TYR c 57 ARG 0.004 0.000 ARG c 35 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 794) hydrogen bonds : angle 2.50972 ( 1964) covalent geometry : bond 0.00390 (13690) covalent geometry : angle 0.57787 (19900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8925 (t0) cc_final: 0.8598 (t0) REVERT: c 63 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (mt) REVERT: c 71 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7392 (mmt-90) REVERT: g 63 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (mt) REVERT: g 64 GLU cc_start: 0.8689 (tp30) cc_final: 0.8303 (tp30) REVERT: g 90 ASP cc_start: 0.7995 (t0) cc_final: 0.7785 (t0) REVERT: g 92 GLU cc_start: 0.8637 (mp0) cc_final: 0.8348 (mp0) REVERT: g 110 ASN cc_start: 0.9123 (t0) cc_final: 0.8839 (p0) REVERT: d 32 LYS cc_start: 0.8774 (tppt) cc_final: 0.8463 (mmmm) REVERT: h 49 ASP cc_start: 0.8604 (m-30) cc_final: 0.8338 (t0) REVERT: h 77 ARG cc_start: 0.9090 (ttm110) cc_final: 0.8642 (mtm-85) REVERT: h 81 TYR cc_start: 0.8836 (m-10) cc_final: 0.8421 (m-10) REVERT: h 83 LYS cc_start: 0.9275 (mptt) cc_final: 0.9005 (mttp) REVERT: h 103 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7995 (tp30) REVERT: a 57 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8787 (ttmt) REVERT: a 82 ASP cc_start: 0.8580 (t0) cc_final: 0.8268 (t0) REVERT: a 88 SER cc_start: 0.9032 (p) cc_final: 0.8754 (t) REVERT: a 91 MET cc_start: 0.8918 (mpp) cc_final: 0.8694 (mmp) REVERT: b 26 ASN cc_start: 0.8942 (m110) cc_final: 0.8605 (m-40) REVERT: f 85 MET cc_start: 0.8997 (mmm) cc_final: 0.8415 (mmm) outliers start: 14 outliers final: 11 residues processed: 159 average time/residue: 0.3125 time to fit residues: 67.1187 Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain g residue 63 LEU Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 94 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 = 0.3895 r_free = 0.3895 target = 0.093124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063846 restraints weight = 39611.539| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.83 r_work: 0.3057 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13690 Z= 0.272 Angle : 0.636 6.907 19900 Z= 0.376 Chirality : 0.037 0.147 2264 Planarity : 0.005 0.041 1388 Dihedral : 32.062 177.725 4484 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.55 % Allowed : 14.33 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.31), residues: 754 helix: 2.30 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS d 107 PHE 0.013 0.001 PHE c 25 TYR 0.024 0.002 TYR b 89 ARG 0.005 0.001 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 794) hydrogen bonds : angle 2.73785 ( 1964) covalent geometry : bond 0.00616 (13690) covalent geometry : angle 0.63586 (19900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.9008 (t0) cc_final: 0.8652 (t0) REVERT: c 63 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9019 (mt) REVERT: c 71 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7533 (mtt90) REVERT: g 90 ASP cc_start: 0.8052 (t0) cc_final: 0.7836 (t0) REVERT: g 92 GLU cc_start: 0.8677 (mp0) cc_final: 0.8413 (mp0) REVERT: d 32 LYS cc_start: 0.8760 (tppt) cc_final: 0.8439 (mmmm) REVERT: d 66 ASP cc_start: 0.8702 (t70) cc_final: 0.8388 (t0) REVERT: h 49 ASP cc_start: 0.8548 (m-30) cc_final: 0.8342 (t0) REVERT: h 81 TYR cc_start: 0.8899 (m-10) cc_final: 0.8434 (m-10) REVERT: h 83 LYS cc_start: 0.9289 (mptt) cc_final: 0.9020 (mttp) REVERT: h 103 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8258 (tp30) REVERT: a 57 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8798 (ttmt) REVERT: a 60 GLU cc_start: 0.8691 (pm20) cc_final: 0.8457 (pm20) REVERT: a 82 ASP cc_start: 0.8604 (t0) cc_final: 0.8300 (t0) REVERT: a 88 SER cc_start: 0.9121 (p) cc_final: 0.8834 (t) outliers start: 16 outliers final: 13 residues processed: 158 average time/residue: 0.3054 time to fit residues: 65.3023 Evaluate side-chains 160 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.094457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065196 restraints weight = 39898.902| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.79 r_work: 0.3141 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13690 Z= 0.193 Angle : 0.602 10.078 19900 Z= 0.358 Chirality : 0.035 0.174 2264 Planarity : 0.004 0.041 1388 Dihedral : 31.713 174.843 4484 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.55 % Allowed : 15.13 % Favored : 82.32 % 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: 2.11 (0.31), residues: 754 helix: 2.42 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS d 80 PHE 0.009 0.001 PHE c 25 TYR 0.012 0.001 TYR d 81 ARG 0.004 0.000 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 794) hydrogen bonds : angle 2.60990 ( 1964) covalent geometry : bond 0.00433 (13690) covalent geometry : angle 0.60199 (19900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8957 (t0) cc_final: 0.8601 (t0) REVERT: c 71 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7543 (mmt-90) REVERT: g 90 ASP cc_start: 0.8052 (t0) cc_final: 0.7743 (t0) REVERT: g 92 GLU cc_start: 0.8711 (mp0) cc_final: 0.8410 (mp0) REVERT: d 32 LYS cc_start: 0.8777 (tppt) cc_final: 0.8461 (mmmm) REVERT: h 49 ASP cc_start: 0.8549 (m-30) cc_final: 0.8328 (t0) REVERT: h 77 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8683 (mtm-85) REVERT: h 81 TYR cc_start: 0.8851 (m-10) cc_final: 0.8366 (m-10) REVERT: h 83 LYS cc_start: 0.9292 (mptt) cc_final: 0.9037 (mttp) REVERT: h 103 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8153 (tp30) REVERT: a 57 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8769 (ttmt) REVERT: a 60 GLU cc_start: 0.8673 (pm20) cc_final: 0.8422 (pm20) REVERT: a 82 ASP cc_start: 0.8522 (t0) cc_final: 0.8233 (t0) REVERT: a 88 SER cc_start: 0.9039 (p) cc_final: 0.8744 (t) REVERT: f 85 MET cc_start: 0.9019 (mmm) cc_final: 0.8469 (mmm) outliers start: 16 outliers final: 13 residues processed: 155 average time/residue: 0.3139 time to fit residues: 66.0410 Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 45 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3951 r_free = 0.3951 target = 0.096080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067321 restraints weight = 39560.649| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.87 r_work: 0.3143 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13690 Z= 0.161 Angle : 0.581 9.483 19900 Z= 0.348 Chirality : 0.033 0.198 2264 Planarity : 0.004 0.040 1388 Dihedral : 31.394 173.039 4484 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % 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: 2.22 (0.31), residues: 754 helix: 2.54 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS d 80 PHE 0.005 0.001 PHE c 25 TYR 0.013 0.001 TYR b 89 ARG 0.005 0.000 ARG d 77 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 794) hydrogen bonds : angle 2.48671 ( 1964) covalent geometry : bond 0.00354 (13690) covalent geometry : angle 0.58084 (19900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8913 (t0) cc_final: 0.8569 (t0) REVERT: c 35 ARG cc_start: 0.8793 (mtm-85) cc_final: 0.8150 (mtm-85) REVERT: g 90 ASP cc_start: 0.7968 (t0) cc_final: 0.7635 (t0) REVERT: g 92 GLU cc_start: 0.8714 (mp0) cc_final: 0.8424 (mp0) REVERT: d 32 LYS cc_start: 0.8773 (tppt) cc_final: 0.8458 (mmmm) REVERT: h 49 ASP cc_start: 0.8468 (m-30) cc_final: 0.8263 (t0) REVERT: h 77 ARG cc_start: 0.9059 (ttm110) cc_final: 0.8663 (mtm-85) REVERT: h 81 TYR cc_start: 0.8820 (m-10) cc_final: 0.8357 (m-10) REVERT: h 83 LYS cc_start: 0.9260 (mptt) cc_final: 0.9003 (mttp) REVERT: a 57 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8779 (ttmt) REVERT: a 60 GLU cc_start: 0.8628 (pm20) cc_final: 0.8272 (pm20) REVERT: a 82 ASP cc_start: 0.8507 (t0) cc_final: 0.8228 (t0) REVERT: a 88 SER cc_start: 0.8985 (p) cc_final: 0.8645 (t) REVERT: a 91 MET cc_start: 0.8903 (mpp) cc_final: 0.8667 (mmp) REVERT: b 26 ASN cc_start: 0.8940 (m110) cc_final: 0.8635 (m-40) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.4559 time to fit residues: 96.3317 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.094877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065681 restraints weight = 40200.279| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.90 r_work: 0.3101 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13690 Z= 0.221 Angle : 0.615 7.443 19900 Z= 0.367 Chirality : 0.035 0.177 2264 Planarity : 0.004 0.042 1388 Dihedral : 31.610 172.616 4484 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.59 % Allowed : 16.08 % Favored : 82.32 % 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: 2.07 (0.31), residues: 754 helix: 2.39 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 76 PHE 0.011 0.001 PHE c 25 TYR 0.032 0.002 TYR b 89 ARG 0.005 0.000 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 794) hydrogen bonds : angle 2.65810 ( 1964) covalent geometry : bond 0.00499 (13690) covalent geometry : angle 0.61536 (19900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 19 ASN cc_start: 0.8935 (t0) cc_final: 0.8575 (t0) REVERT: c 35 ARG cc_start: 0.8828 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: g 64 GLU cc_start: 0.8714 (tp30) cc_final: 0.8221 (tp30) REVERT: g 90 ASP cc_start: 0.8039 (t0) cc_final: 0.7739 (t0) REVERT: g 92 GLU cc_start: 0.8715 (mp0) cc_final: 0.8478 (mp0) REVERT: d 32 LYS cc_start: 0.8787 (tppt) cc_final: 0.8466 (mmmm) REVERT: h 49 ASP cc_start: 0.8524 (m-30) cc_final: 0.8305 (t0) REVERT: h 77 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8676 (mtm-85) REVERT: h 81 TYR cc_start: 0.8838 (m-10) cc_final: 0.8334 (m-10) REVERT: h 83 LYS cc_start: 0.9257 (mptt) cc_final: 0.9006 (mttp) REVERT: h 103 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8074 (tp30) REVERT: a 57 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8837 (ttmt) REVERT: a 60 GLU cc_start: 0.8669 (pm20) cc_final: 0.8312 (pm20) REVERT: a 82 ASP cc_start: 0.8593 (t0) cc_final: 0.8309 (t0) REVERT: a 88 SER cc_start: 0.9048 (p) cc_final: 0.8762 (t) outliers start: 10 outliers final: 10 residues processed: 148 average time/residue: 0.3739 time to fit residues: 74.8185 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 81 TYR Chi-restraints excluded: chain h residue 45 GLN Chi-restraints excluded: chain h residue 67 ILE Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain f residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 70 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 76 HIS ** 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 = 0.3937 r_free = 0.3937 target = 0.095371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066911 restraints weight = 39515.016| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.87 r_work: 0.3125 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13690 Z= 0.180 Angle : 0.595 8.175 19900 Z= 0.356 Chirality : 0.034 0.201 2264 Planarity : 0.004 0.040 1388 Dihedral : 31.506 171.692 4484 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.75 % Allowed : 16.40 % Favored : 81.85 % 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: 2.04 (0.31), residues: 754 helix: 2.39 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.48 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS d 80 PHE 0.007 0.001 PHE c 25 TYR 0.052 0.002 TYR b 89 ARG 0.005 0.000 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 794) hydrogen bonds : angle 2.60737 ( 1964) covalent geometry : bond 0.00402 (13690) covalent geometry : angle 0.59547 (19900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.65 seconds wall clock time: 112 minutes 39.51 seconds (6759.51 seconds total)