Starting phenix.real_space_refine on Sat Aug 23 11:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614.map" model { file = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euj_28614/08_2025/8euj_28614_neut.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.104 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 292 5.49 5 S 12 5.16 5 C 6591 2.51 5 N 2205 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 765 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "b" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 782 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU O 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU O 22 " occ=0.00 residue: pdb=" N ARG O 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG O 23 " occ=0.00 Time building chain proxies: 3.40, per 1000 atoms: 0.29 Number of scatterers: 11913 At special positions: 0 Unit cell: (116.065, 120.24, 104.375, 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 292 15.00 O 2813 8.00 N 2205 7.00 C 6591 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: 1.01 Conformation dependent library (CDL) restraints added in 457.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 73.0% alpha, 1.6% beta 147 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.765A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.520A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.545A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.779A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 29 removed outlier: 4.088A pdb=" N ILE O 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 Processing helix chain 'O' and resid 50 through 76 removed outlier: 4.044A pdb=" N ASP O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 93 removed outlier: 3.745A pdb=" N VAL O 86 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 22 Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 45 through 72 removed outlier: 4.141A pdb=" N VAL a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 89 removed outlier: 3.666A pdb=" N ASN a 89 " --> pdb=" O LEU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'b' and resid 34 through 46 removed outlier: 4.186A pdb=" N VAL b 38 " --> pdb=" O TYR b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 80 Processing helix chain 'b' and resid 87 through 99 removed outlier: 3.759A pdb=" N LEU b 98 " --> pdb=" O ALA b 94 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU b 99 " --> pdb=" O VAL b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 121 removed outlier: 3.884A pdb=" N ALA b 121 " --> pdb=" O LYS b 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 57 Processing helix chain 'f' and resid 63 through 79 removed outlier: 3.955A pdb=" N PHE f 67 " --> pdb=" O ARG f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 114 Processing helix chain 'f' and resid 121 through 131 Processing helix chain 'h' and resid 24 through 29 removed outlier: 3.529A pdb=" N GLN h 27 " --> pdb=" O ASP h 24 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 49 through 76 removed outlier: 3.612A pdb=" N ALA h 76 " --> pdb=" O TYR h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 94 removed outlier: 3.823A pdb=" N VAL h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 22 removed outlier: 3.776A pdb=" N ARG k 20 " --> pdb=" O THR k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 36 removed outlier: 3.995A pdb=" N VAL k 30 " --> pdb=" O PRO k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 74 removed outlier: 4.404A pdb=" N VAL k 49 " --> pdb=" O ALA k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 88 Processing helix chain 'k' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 51 removed outlier: 7.857A pdb=" N GLY H 50 " --> pdb=" O ILE k 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 96 through 97 removed outlier: 6.869A pdb=" N THR O 96 " --> pdb=" O THR k 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'f' and resid 83 through 84 removed outlier: 7.148A pdb=" N ARG f 83 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 390 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 4499 1.46 - 1.58: 4978 1.58 - 1.71: 585 1.71 - 1.83: 22 Bond restraints: 12721 Sorted by residual: bond pdb=" C ILE a 79 " pdb=" N PRO a 80 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.08e-02 8.57e+03 9.40e+00 bond pdb=" CB PRO a 109 " pdb=" CG PRO a 109 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.96e+00 bond pdb=" CB ASN k 73 " pdb=" CG ASN k 73 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.15e+00 bond pdb=" CB ASN H 60 " pdb=" CG ASN H 60 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.91e+00 bond pdb=" CB ASN a 38 " pdb=" CG ASN a 38 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.76e+00 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 18248 4.68 - 9.36: 170 9.36 - 14.05: 26 14.05 - 18.73: 3 18.73 - 23.41: 1 Bond angle restraints: 18448 Sorted by residual: angle pdb=" CA PRO a 109 " pdb=" N PRO a 109 " pdb=" CD PRO a 109 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA LEU f 65 " pdb=" CB LEU f 65 " pdb=" CG LEU f 65 " ideal model delta sigma weight residual 116.30 139.71 -23.41 3.50e+00 8.16e-02 4.47e+01 angle pdb=" CA PRO f 43 " pdb=" N PRO f 43 " pdb=" CD PRO f 43 " ideal model delta sigma weight residual 112.00 103.70 8.30 1.40e+00 5.10e-01 3.51e+01 angle pdb=" CA LYS M 64 " pdb=" CB LYS M 64 " pdb=" CG LYS M 64 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.51e+01 angle pdb=" CA ARG b 89 " pdb=" CB ARG b 89 " pdb=" CG ARG b 89 " ideal model delta sigma weight residual 114.10 125.01 -10.91 2.00e+00 2.50e-01 2.98e+01 ... (remaining 18443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3951 18.00 - 36.00: 1366 36.00 - 54.00: 1251 54.00 - 72.00: 355 72.00 - 90.00: 52 Dihedral angle restraints: 6975 sinusoidal: 4809 harmonic: 2166 Sorted by residual: dihedral pdb=" CA ILE O 50 " pdb=" C ILE O 50 " pdb=" N TYR O 51 " pdb=" CA TYR O 51 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU b 97 " pdb=" C LEU b 97 " pdb=" N LEU b 98 " pdb=" CA LEU b 98 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU a 108 " pdb=" C LEU a 108 " pdb=" N PRO a 109 " pdb=" CA PRO a 109 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1866 0.083 - 0.167: 213 0.167 - 0.250: 17 0.250 - 0.334: 4 0.334 - 0.417: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE H 58 " pdb=" CA ILE H 58 " pdb=" CG1 ILE H 58 " pdb=" CG2 ILE H 58 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CB VAL H 41 " pdb=" CA VAL H 41 " pdb=" CG1 VAL H 41 " pdb=" CG2 VAL H 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2101 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 108 " -0.106 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO a 109 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO a 109 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO a 109 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG f 42 " 0.069 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO f 43 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO f 43 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO f 43 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 88 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR h 88 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR h 88 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR h 88 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR h 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR h 88 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 88 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR h 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1827 2.77 - 3.30: 10431 3.30 - 3.83: 25130 3.83 - 4.37: 27389 4.37 - 4.90: 37898 Nonbonded interactions: 102675 Sorted by model distance: nonbonded pdb=" O LEU a 55 " pdb=" OG1 THR a 59 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP b 65 " pdb=" OH TYR h 98 " model vdw 2.259 3.040 nonbonded pdb=" OP1 DT J 18 " pdb=" NZ LYS M 64 " model vdw 2.267 3.120 nonbonded pdb=" O TYR a 39 " pdb=" OG SER b 75 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP H 65 " pdb=" OH TYR O 98 " model vdw 2.294 3.040 ... (remaining 102670 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 'H' and resid 30 through 121) selection = (chain 'b' and (resid 30 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } ncs_group { reference = (chain 'M' and (resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 135)) selection = (chain 'f' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 133 or (resid 134 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'O' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = chain 'h' } ncs_group { reference = (chain 'a' and resid 15 through 118) selection = chain 'k' } 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=0.00 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: 11.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.870 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 0.141 12721 Z= 0.271 Angle : 1.221 23.411 18448 Z= 0.645 Chirality : 0.057 0.417 2104 Planarity : 0.011 0.150 1319 Dihedral : 30.772 89.997 5577 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 40.55 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.27), residues: 730 helix: -1.65 (0.19), residues: 517 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG k 71 TYR 0.065 0.005 TYR h 88 PHE 0.056 0.004 PHE O 61 HIS 0.011 0.002 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00608 (12721) covalent geometry : angle 1.22062 (18448) hydrogen bonds : bond 0.10322 ( 744) hydrogen bonds : angle 5.25028 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7442 (mm-30) REVERT: a 112 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6424 (tm-30) REVERT: b 73 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7758 (mm-30) REVERT: b 76 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8527 (ttm110) REVERT: f 90 MET cc_start: 0.8427 (mmm) cc_final: 0.8214 (mmm) REVERT: k 35 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8339 (mpp80) REVERT: k 71 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8224 (mtt90) REVERT: k 91 GLU cc_start: 0.8103 (pp20) cc_final: 0.7599 (pp20) REVERT: k 92 GLU cc_start: 0.7888 (pm20) cc_final: 0.7657 (pm20) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1468 time to fit residues: 52.8810 Evaluate side-chains 258 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 125 GLN a 73 ASN b 79 HIS k 82 HIS k 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.097640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.078971 restraints weight = 48812.978| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.21 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12721 Z= 0.170 Angle : 0.726 16.952 18448 Z= 0.412 Chirality : 0.037 0.208 2104 Planarity : 0.006 0.076 1319 Dihedral : 32.321 89.678 4127 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.07 % Allowed : 33.39 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.28), residues: 730 helix: -0.25 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 71 TYR 0.038 0.002 TYR O 88 PHE 0.012 0.001 PHE H 67 HIS 0.012 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (12721) covalent geometry : angle 0.72646 (18448) hydrogen bonds : bond 0.04775 ( 744) hydrogen bonds : angle 3.75768 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 LYS cc_start: 0.9035 (pttm) cc_final: 0.8679 (pttm) REVERT: H 76 ARG cc_start: 0.9147 (ptp-110) cc_final: 0.8932 (ptp90) REVERT: M 94 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: M 131 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7576 (ptp-170) REVERT: b 76 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8733 (ttm110) REVERT: f 129 ARG cc_start: 0.8753 (tpt90) cc_final: 0.8404 (tpt90) REVERT: k 35 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8432 (mpp80) REVERT: k 91 GLU cc_start: 0.8337 (pp20) cc_final: 0.7944 (pp20) outliers start: 25 outliers final: 17 residues processed: 271 average time/residue: 0.1273 time to fit residues: 45.6975 Evaluate side-chains 254 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 84 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN k 24 GLN k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.094549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.075692 restraints weight = 50235.548| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.15 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12721 Z= 0.198 Angle : 0.725 14.692 18448 Z= 0.414 Chirality : 0.038 0.163 2104 Planarity : 0.006 0.061 1319 Dihedral : 32.256 88.714 4127 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.51 % Allowed : 31.43 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.29), residues: 730 helix: 0.33 (0.21), residues: 531 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 71 TYR 0.037 0.002 TYR O 88 PHE 0.010 0.002 PHE b 62 HIS 0.020 0.002 HIS b 79 Details of bonding type rmsd covalent geometry : bond 0.00436 (12721) covalent geometry : angle 0.72538 (18448) hydrogen bonds : bond 0.05136 ( 744) hydrogen bonds : angle 3.64097 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7745 (mm-30) REVERT: a 33 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8994 (mm) REVERT: a 65 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8154 (mm) REVERT: a 95 LYS cc_start: 0.9346 (ttmm) cc_final: 0.9039 (mtpp) REVERT: b 64 ASN cc_start: 0.8924 (m-40) cc_final: 0.8675 (m-40) REVERT: b 76 ARG cc_start: 0.9001 (ttm110) cc_final: 0.8799 (ttm110) REVERT: b 113 LYS cc_start: 0.7813 (pptt) cc_final: 0.7607 (pptt) REVERT: k 24 GLN cc_start: 0.7013 (tp40) cc_final: 0.6462 (tt0) REVERT: k 35 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8434 (mpp80) REVERT: k 61 GLU cc_start: 0.8202 (tp30) cc_final: 0.7909 (tp30) REVERT: k 91 GLU cc_start: 0.8559 (pp20) cc_final: 0.8082 (pp20) outliers start: 40 outliers final: 27 residues processed: 260 average time/residue: 0.1304 time to fit residues: 45.3991 Evaluate side-chains 259 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN a 73 ASN a 112 GLN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN k 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.095910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.076753 restraints weight = 49246.078| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.14 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12721 Z= 0.174 Angle : 0.702 13.045 18448 Z= 0.401 Chirality : 0.037 0.174 2104 Planarity : 0.005 0.059 1319 Dihedral : 32.088 89.987 4127 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.68 % Allowed : 32.41 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.30), residues: 730 helix: 0.58 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 71 TYR 0.042 0.002 TYR O 88 PHE 0.012 0.001 PHE b 62 HIS 0.011 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (12721) covalent geometry : angle 0.70227 (18448) hydrogen bonds : bond 0.04665 ( 744) hydrogen bonds : angle 3.51870 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8918 (tptt) cc_final: 0.8614 (tppt) REVERT: H 40 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8467 (ptpp) REVERT: H 92 GLN cc_start: 0.8594 (tp40) cc_final: 0.8289 (tp40) REVERT: M 105 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7662 (mm-30) REVERT: a 33 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8968 (mm) REVERT: a 42 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7590 (ttp80) REVERT: a 65 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8217 (mm) REVERT: a 95 LYS cc_start: 0.9384 (ttmm) cc_final: 0.9053 (mtpp) REVERT: b 76 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8551 (ttm110) REVERT: f 83 ARG cc_start: 0.8025 (mmp80) cc_final: 0.7820 (mmp80) REVERT: f 90 MET cc_start: 0.8442 (mmp) cc_final: 0.8136 (mmm) REVERT: h 27 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7643 (tp-100) REVERT: h 66 ILE cc_start: 0.9010 (pt) cc_final: 0.8585 (mt) REVERT: h 72 TYR cc_start: 0.7755 (t80) cc_final: 0.7473 (t80) REVERT: k 23 LEU cc_start: 0.7580 (mt) cc_final: 0.7258 (mp) REVERT: k 35 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8400 (mpp80) REVERT: k 91 GLU cc_start: 0.8612 (pp20) cc_final: 0.8036 (pp20) outliers start: 41 outliers final: 26 residues processed: 275 average time/residue: 0.1195 time to fit residues: 44.2394 Evaluate side-chains 266 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 112 GLN k 24 GLN k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.095566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.076578 restraints weight = 48893.509| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.09 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12721 Z= 0.177 Angle : 0.719 14.419 18448 Z= 0.406 Chirality : 0.037 0.184 2104 Planarity : 0.005 0.059 1319 Dihedral : 32.042 89.217 4127 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.35 % Allowed : 33.88 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.30), residues: 730 helix: 0.83 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 71 TYR 0.042 0.002 TYR O 88 PHE 0.014 0.001 PHE b 62 HIS 0.007 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00388 (12721) covalent geometry : angle 0.71913 (18448) hydrogen bonds : bond 0.04704 ( 744) hydrogen bonds : angle 3.47680 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8655 (tp40) cc_final: 0.8135 (tp40) REVERT: M 105 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7706 (mm-30) REVERT: a 33 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8974 (mm) REVERT: a 42 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7631 (ttp80) REVERT: a 95 LYS cc_start: 0.9388 (ttmm) cc_final: 0.9042 (mtpp) REVERT: b 30 ARG cc_start: 0.6385 (mmm160) cc_final: 0.6149 (mpt180) REVERT: b 64 ASN cc_start: 0.8721 (m-40) cc_final: 0.8510 (m110) REVERT: b 76 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8604 (ttm110) REVERT: b 113 LYS cc_start: 0.7745 (pptt) cc_final: 0.7533 (pptt) REVERT: f 90 MET cc_start: 0.8486 (mmp) cc_final: 0.8283 (mmm) REVERT: h 66 ILE cc_start: 0.8985 (pt) cc_final: 0.8601 (mt) REVERT: h 72 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7508 (t80) REVERT: k 23 LEU cc_start: 0.7654 (mt) cc_final: 0.7267 (mp) REVERT: k 24 GLN cc_start: 0.7289 (tp40) cc_final: 0.6408 (tt0) REVERT: k 35 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8444 (mpp80) outliers start: 39 outliers final: 29 residues processed: 268 average time/residue: 0.1387 time to fit residues: 49.9552 Evaluate side-chains 272 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.093024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.074235 restraints weight = 49424.816| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.02 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12721 Z= 0.218 Angle : 0.750 13.499 18448 Z= 0.423 Chirality : 0.039 0.182 2104 Planarity : 0.006 0.058 1319 Dihedral : 32.231 88.961 4127 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 8.31 % Allowed : 33.39 % Favored : 58.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.30), residues: 730 helix: 0.79 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 71 TYR 0.045 0.003 TYR O 88 PHE 0.014 0.002 PHE b 62 HIS 0.008 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (12721) covalent geometry : angle 0.74995 (18448) hydrogen bonds : bond 0.05475 ( 744) hydrogen bonds : angle 3.67338 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8684 (tp40) cc_final: 0.8154 (tp40) REVERT: H 102 GLU cc_start: 0.8354 (pp20) cc_final: 0.8080 (pp20) REVERT: M 105 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7747 (mm-30) REVERT: a 33 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8977 (mm) REVERT: a 42 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7711 (ttp80) REVERT: a 64 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: a 65 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8279 (mm) REVERT: b 76 ARG cc_start: 0.8921 (ttm110) cc_final: 0.8635 (ttm110) REVERT: b 113 LYS cc_start: 0.7805 (pptt) cc_final: 0.7605 (pttp) REVERT: h 27 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7460 (tp-100) REVERT: h 72 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7540 (t80) REVERT: k 23 LEU cc_start: 0.7717 (mt) cc_final: 0.7336 (mp) REVERT: k 24 GLN cc_start: 0.7291 (tp40) cc_final: 0.6686 (tt0) REVERT: k 35 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8445 (mpp80) outliers start: 51 outliers final: 35 residues processed: 267 average time/residue: 0.1358 time to fit residues: 48.8498 Evaluate side-chains 269 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 110 CYS Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN a 112 GLN k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.094845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.075716 restraints weight = 49370.387| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.05 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12721 Z= 0.181 Angle : 0.751 12.849 18448 Z= 0.420 Chirality : 0.038 0.189 2104 Planarity : 0.006 0.058 1319 Dihedral : 32.145 89.303 4127 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 7.49 % Allowed : 34.85 % Favored : 57.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.30), residues: 730 helix: 0.82 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG k 71 TYR 0.048 0.003 TYR O 88 PHE 0.016 0.001 PHE b 62 HIS 0.007 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (12721) covalent geometry : angle 0.75088 (18448) hydrogen bonds : bond 0.04727 ( 744) hydrogen bonds : angle 3.54385 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8718 (tp40) cc_final: 0.8120 (tp40) REVERT: H 102 GLU cc_start: 0.8291 (pp20) cc_final: 0.8043 (pp20) REVERT: M 105 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7786 (mm-30) REVERT: M 133 GLU cc_start: 0.7855 (mp0) cc_final: 0.7231 (pm20) REVERT: O 44 LYS cc_start: 0.8273 (tptm) cc_final: 0.8013 (tptt) REVERT: a 33 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8961 (mm) REVERT: a 42 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7702 (ttp80) REVERT: a 65 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8314 (mm) REVERT: b 76 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8583 (ttm110) REVERT: b 113 LYS cc_start: 0.7849 (pptt) cc_final: 0.7574 (pttp) REVERT: h 27 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7487 (tp-100) REVERT: h 66 ILE cc_start: 0.8992 (pt) cc_final: 0.8689 (mt) REVERT: h 72 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7476 (t80) REVERT: k 24 GLN cc_start: 0.7033 (tp40) cc_final: 0.6800 (tt0) REVERT: k 35 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8457 (mpp80) outliers start: 46 outliers final: 32 residues processed: 272 average time/residue: 0.1306 time to fit residues: 47.4146 Evaluate side-chains 279 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.093952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.074913 restraints weight = 49362.175| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.04 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12721 Z= 0.201 Angle : 0.760 12.820 18448 Z= 0.426 Chirality : 0.038 0.211 2104 Planarity : 0.006 0.061 1319 Dihedral : 32.153 89.777 4127 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.00 % Allowed : 35.67 % Favored : 57.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.30), residues: 730 helix: 0.86 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG k 71 TYR 0.058 0.003 TYR O 88 PHE 0.019 0.002 PHE b 62 HIS 0.004 0.001 HIS h 75 Details of bonding type rmsd covalent geometry : bond 0.00447 (12721) covalent geometry : angle 0.75986 (18448) hydrogen bonds : bond 0.05098 ( 744) hydrogen bonds : angle 3.63118 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8719 (tp40) cc_final: 0.8341 (tp40) REVERT: H 102 GLU cc_start: 0.8353 (pp20) cc_final: 0.8125 (pp20) REVERT: M 105 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7765 (mm-30) REVERT: M 133 GLU cc_start: 0.7770 (mp0) cc_final: 0.7147 (pm20) REVERT: O 44 LYS cc_start: 0.8258 (tptm) cc_final: 0.8019 (tptt) REVERT: a 33 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8952 (mm) REVERT: a 42 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7729 (ttp80) REVERT: a 65 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8342 (mm) REVERT: b 76 ARG cc_start: 0.8911 (ttm110) cc_final: 0.8642 (ttm110) REVERT: b 113 LYS cc_start: 0.7765 (pptt) cc_final: 0.7559 (pttp) REVERT: h 27 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7441 (tp-100) REVERT: h 66 ILE cc_start: 0.9026 (pt) cc_final: 0.8688 (mt) REVERT: h 72 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7486 (t80) REVERT: k 24 GLN cc_start: 0.7264 (tp40) cc_final: 0.6832 (tt0) REVERT: k 35 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8430 (mpp80) outliers start: 43 outliers final: 31 residues processed: 258 average time/residue: 0.1370 time to fit residues: 46.7741 Evaluate side-chains 275 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.094603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.075627 restraints weight = 48955.881| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.02 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12721 Z= 0.188 Angle : 0.781 13.363 18448 Z= 0.432 Chirality : 0.039 0.232 2104 Planarity : 0.006 0.061 1319 Dihedral : 32.171 88.890 4127 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.84 % Allowed : 35.83 % Favored : 57.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.30), residues: 730 helix: 0.86 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.61 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG k 71 TYR 0.058 0.003 TYR O 88 PHE 0.021 0.001 PHE b 62 HIS 0.004 0.001 HIS b 79 Details of bonding type rmsd covalent geometry : bond 0.00420 (12721) covalent geometry : angle 0.78053 (18448) hydrogen bonds : bond 0.04789 ( 744) hydrogen bonds : angle 3.60675 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 GLN cc_start: 0.8721 (tp40) cc_final: 0.7932 (tp40) REVERT: H 102 GLU cc_start: 0.8300 (pp20) cc_final: 0.8086 (pp20) REVERT: M 105 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7816 (mm-30) REVERT: M 133 GLU cc_start: 0.7739 (mp0) cc_final: 0.7346 (pm20) REVERT: O 44 LYS cc_start: 0.8205 (tptm) cc_final: 0.7932 (tptt) REVERT: a 33 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8964 (mm) REVERT: a 42 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7879 (mtp85) REVERT: a 65 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8327 (mm) REVERT: b 73 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8319 (mm-30) REVERT: b 76 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8522 (ttm110) REVERT: b 113 LYS cc_start: 0.7702 (pptt) cc_final: 0.7502 (pttp) REVERT: h 27 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7364 (tp-100) REVERT: h 66 ILE cc_start: 0.9021 (pt) cc_final: 0.8618 (tt) REVERT: h 72 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7419 (t80) REVERT: h 100 PHE cc_start: 0.8595 (m-80) cc_final: 0.8325 (m-80) REVERT: k 24 GLN cc_start: 0.7263 (tp40) cc_final: 0.6893 (tt0) REVERT: k 35 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8388 (mpp80) outliers start: 42 outliers final: 31 residues processed: 265 average time/residue: 0.1347 time to fit residues: 47.5174 Evaluate side-chains 272 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 110 CYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.092700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.073888 restraints weight = 49798.549| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.02 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12721 Z= 0.225 Angle : 0.806 14.428 18448 Z= 0.445 Chirality : 0.040 0.238 2104 Planarity : 0.006 0.063 1319 Dihedral : 32.259 89.678 4127 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.51 % Allowed : 35.99 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.30), residues: 730 helix: 0.77 (0.21), residues: 529 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 71 TYR 0.054 0.003 TYR O 88 PHE 0.019 0.002 PHE b 62 HIS 0.005 0.001 HIS h 75 Details of bonding type rmsd covalent geometry : bond 0.00504 (12721) covalent geometry : angle 0.80595 (18448) hydrogen bonds : bond 0.05650 ( 744) hydrogen bonds : angle 3.77809 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: H 30 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6554 (mtt180) REVERT: H 102 GLU cc_start: 0.8369 (pp20) cc_final: 0.8160 (pp20) REVERT: H 117 LYS cc_start: 0.9360 (tttt) cc_final: 0.9083 (tmtt) REVERT: M 105 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7836 (mm-30) REVERT: M 133 GLU cc_start: 0.7733 (mp0) cc_final: 0.7297 (pm20) REVERT: a 33 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8969 (mm) REVERT: a 42 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.8008 (ttp80) REVERT: a 65 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8343 (mm) REVERT: a 112 GLN cc_start: 0.6767 (tp40) cc_final: 0.6565 (tp40) REVERT: b 76 ARG cc_start: 0.8953 (ttm110) cc_final: 0.8654 (ttm110) REVERT: f 77 ASP cc_start: 0.8768 (m-30) cc_final: 0.8460 (m-30) REVERT: f 106 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7367 (t0) REVERT: h 66 ILE cc_start: 0.9046 (pt) cc_final: 0.8673 (mt) REVERT: h 72 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7490 (t80) REVERT: k 24 GLN cc_start: 0.7435 (tp40) cc_final: 0.6972 (tt0) REVERT: k 35 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8408 (mpp80) outliers start: 40 outliers final: 33 residues processed: 254 average time/residue: 0.1253 time to fit residues: 43.0765 Evaluate side-chains 275 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 110 CYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 GLU Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 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 = 0.4126 r_free = 0.4126 target = 0.095771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.076948 restraints weight = 48906.720| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.05 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12721 Z= 0.176 Angle : 0.799 13.623 18448 Z= 0.436 Chirality : 0.039 0.210 2104 Planarity : 0.006 0.066 1319 Dihedral : 32.132 88.922 4127 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.86 % Allowed : 37.30 % Favored : 56.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.30), residues: 730 helix: 0.94 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.54 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG k 71 TYR 0.049 0.003 TYR O 88 PHE 0.023 0.001 PHE b 62 HIS 0.003 0.001 HIS O 75 Details of bonding type rmsd covalent geometry : bond 0.00390 (12721) covalent geometry : angle 0.79912 (18448) hydrogen bonds : bond 0.04508 ( 744) hydrogen bonds : angle 3.55015 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.55 seconds wall clock time: 42 minutes 46.93 seconds (2566.93 seconds total)