Starting phenix.real_space_refine on Sat Aug 23 16:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.map" model { file = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pep_17634/08_2025/8pep_17634.cif" } resolution = 3.33 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= 0.001 sd= 0.011 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 293 5.49 5 S 15 5.16 5 C 7599 2.51 5 N 2518 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s 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: 13492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "'] Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3014 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.21 Number of scatterers: 13492 At special positions: 0 Unit cell: (95.019, 120.024, 138.361, 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 15 16.00 P 293 15.00 O 3067 8.00 N 2518 7.00 C 7599 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: 0.81 Conformation dependent library (CDL) restraints added in 373.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 59.6% alpha, 6.2% beta 135 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.532A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.613A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.890A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.551A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.892A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.571A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.976A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.249A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.853A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.565A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.330A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.263A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'L' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.660A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.407A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.251A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.411A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 4.040A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.984A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.23 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: 3179 1.34 - 1.46: 4341 1.46 - 1.58: 6223 1.58 - 1.70: 584 1.70 - 1.82: 30 Bond restraints: 14357 Sorted by residual: bond pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C M2L A 36 " pdb=" O M2L A 36 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C3' DG J 63 " pdb=" O3' DG J 63 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.62e-02 3.81e+03 1.70e+00 ... (remaining 14352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 20435 2.72 - 5.44: 168 5.44 - 8.16: 11 8.16 - 10.88: 3 10.88 - 13.60: 2 Bond angle restraints: 20619 Sorted by residual: angle pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " pdb=" CD LYS K 65 " ideal model delta sigma weight residual 111.30 124.90 -13.60 2.30e+00 1.89e-01 3.50e+01 angle pdb=" CA LYS K 65 " pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " ideal model delta sigma weight residual 114.10 125.68 -11.58 2.00e+00 2.50e-01 3.35e+01 angle pdb=" C MET L 1 " pdb=" CA MET L 1 " pdb=" CB MET L 1 " ideal model delta sigma weight residual 110.10 118.38 -8.28 1.90e+00 2.77e-01 1.90e+01 angle pdb=" C LYS K 65 " pdb=" CA LYS K 65 " pdb=" CB LYS K 65 " ideal model delta sigma weight residual 110.79 104.32 6.47 1.66e+00 3.63e-01 1.52e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 122.07 127.27 -5.20 1.43e+00 4.89e-01 1.32e+01 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 6267 35.32 - 70.63: 1598 70.63 - 105.95: 41 105.95 - 141.26: 3 141.26 - 176.58: 4 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" CD M2L A 36 " pdb=" CE M2L A 36 " pdb=" NZ M2L A 36 " pdb=" CM1 M2L A 36 " ideal model delta sinusoidal sigma weight residual 66.23 -97.70 163.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 43.42 176.58 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.58 -164.58 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1969 0.061 - 0.123: 319 0.123 - 0.184: 26 0.184 - 0.245: 6 0.245 - 0.307: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CB ILE L 58 " pdb=" CA ILE L 58 " pdb=" CG1 ILE L 58 " pdb=" CG2 ILE L 58 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS K 65 " pdb=" N LYS K 65 " pdb=" C LYS K 65 " pdb=" CB LYS K 65 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ARG F 23 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 114 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ALA D 114 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA D 114 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL D 115 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 55 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG F 55 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG F 55 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY F 56 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 246 2.65 - 3.22: 11181 3.22 - 3.78: 24818 3.78 - 4.34: 32052 4.34 - 4.90: 46603 Nonbonded interactions: 114900 Sorted by model distance: nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.092 3.040 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.100 3.120 nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.235 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.244 3.120 ... (remaining 114895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } 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: 0.810 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.840 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.004 0.050 14357 Z= 0.177 Angle : 0.716 13.598 20619 Z= 0.422 Chirality : 0.045 0.307 2322 Planarity : 0.007 0.086 1605 Dihedral : 28.764 176.578 6157 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % 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: 0.85 (0.27), residues: 913 helix: 1.74 (0.22), residues: 548 sheet: -2.95 (0.69), residues: 34 loop : -1.06 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 129 TYR 0.035 0.002 TYR K 61 PHE 0.036 0.002 PHE C 25 TRP 0.008 0.001 TRP K 21 HIS 0.007 0.001 HIS L 20 Details of bonding type rmsd covalent geometry : bond 0.00381 (14357) covalent geometry : angle 0.71631 (20619) hydrogen bonds : bond 0.19360 ( 771) hydrogen bonds : angle 6.29768 ( 1940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8596 (mtmm) REVERT: G 38 ASN cc_start: 0.7909 (m-40) cc_final: 0.7453 (m-40) REVERT: K 52 PHE cc_start: 0.8284 (m-10) cc_final: 0.8077 (m-80) REVERT: K 78 ASN cc_start: 0.9218 (m-40) cc_final: 0.8985 (m-40) REVERT: L 20 HIS cc_start: 0.7653 (m-70) cc_final: 0.7016 (m170) REVERT: L 59 PHE cc_start: 0.8454 (m-80) cc_final: 0.7894 (m-80) REVERT: L 77 PHE cc_start: 0.8300 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1733 time to fit residues: 35.2465 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 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 = 0.3537 r_free = 0.3537 target = 0.063422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041554 restraints weight = 65002.082| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.94 r_work: 0.2621 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14357 Z= 0.174 Angle : 0.598 9.348 20619 Z= 0.346 Chirality : 0.036 0.191 2322 Planarity : 0.005 0.041 1605 Dihedral : 31.262 179.948 4250 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.25 % Allowed : 7.48 % Favored : 92.27 % 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: 1.44 (0.28), residues: 913 helix: 2.21 (0.22), residues: 563 sheet: -2.67 (0.66), residues: 42 loop : -0.91 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 74 TYR 0.028 0.002 TYR L 61 PHE 0.013 0.001 PHE C 25 TRP 0.017 0.002 TRP L 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00382 (14357) covalent geometry : angle 0.59827 (20619) hydrogen bonds : bond 0.04432 ( 771) hydrogen bonds : angle 3.35615 ( 1940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7555 (t-90) cc_final: 0.7340 (t-90) REVERT: A 73 GLU cc_start: 0.8860 (tt0) cc_final: 0.8548 (tt0) REVERT: C 92 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 30 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7845 (ptt-90) REVERT: D 56 MET cc_start: 0.9029 (tpp) cc_final: 0.8377 (tpp) REVERT: D 76 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8423 (ttm110) REVERT: E 56 LYS cc_start: 0.9505 (mtpp) cc_final: 0.9075 (mtmm) REVERT: F 52 GLU cc_start: 0.8138 (mp0) cc_final: 0.7928 (pm20) REVERT: G 64 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8737 (tm-30) REVERT: G 73 ASN cc_start: 0.9538 (t0) cc_final: 0.9171 (t0) REVERT: G 104 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8865 (mm-40) REVERT: K 1 MET cc_start: 0.2440 (ptp) cc_final: 0.1575 (pmm) REVERT: K 52 PHE cc_start: 0.8619 (m-10) cc_final: 0.8314 (m-80) REVERT: K 53 LEU cc_start: 0.9155 (tt) cc_final: 0.8885 (mp) REVERT: K 78 ASN cc_start: 0.9470 (m-40) cc_final: 0.9216 (p0) REVERT: L 40 LEU cc_start: 0.7141 (tp) cc_final: 0.6730 (tt) REVERT: L 77 PHE cc_start: 0.8179 (t80) cc_final: 0.7565 (t80) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1260 time to fit residues: 17.9305 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.062911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.040926 restraints weight = 66120.117| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.99 r_work: 0.2606 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14357 Z= 0.172 Angle : 0.558 7.044 20619 Z= 0.327 Chirality : 0.035 0.183 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.796 170.638 4250 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.25 % Allowed : 9.76 % Favored : 89.99 % 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: 1.71 (0.28), residues: 913 helix: 2.46 (0.22), residues: 564 sheet: -2.09 (0.67), residues: 45 loop : -0.96 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.011 0.001 TYR L 61 PHE 0.009 0.001 PHE C 25 TRP 0.021 0.003 TRP L 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (14357) covalent geometry : angle 0.55814 (20619) hydrogen bonds : bond 0.04028 ( 771) hydrogen bonds : angle 3.20198 ( 1940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8837 (tt0) cc_final: 0.8508 (tt0) REVERT: A 97 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8777 (mt-10) REVERT: A 120 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: A 125 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8741 (mm-40) REVERT: C 90 ASP cc_start: 0.8449 (t0) cc_final: 0.8240 (t0) REVERT: D 76 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8350 (ttm110) REVERT: E 56 LYS cc_start: 0.9553 (mtpp) cc_final: 0.9175 (mtmm) REVERT: G 73 ASN cc_start: 0.9585 (t0) cc_final: 0.9162 (t0) REVERT: K 1 MET cc_start: 0.3986 (ptp) cc_final: 0.3160 (pmm) REVERT: K 52 PHE cc_start: 0.8635 (m-10) cc_final: 0.8280 (m-80) REVERT: K 78 ASN cc_start: 0.9471 (m-40) cc_final: 0.8993 (p0) REVERT: K 79 GLU cc_start: 0.9504 (pt0) cc_final: 0.9162 (pm20) REVERT: L 20 HIS cc_start: 0.5874 (m170) cc_final: 0.5310 (m-70) REVERT: L 77 PHE cc_start: 0.8314 (t80) cc_final: 0.7240 (t80) outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.1345 time to fit residues: 18.3923 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** 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 = 0.3471 r_free = 0.3471 target = 0.060472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.038266 restraints weight = 65634.777| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.91 r_work: 0.2515 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14357 Z= 0.279 Angle : 0.624 9.203 20619 Z= 0.359 Chirality : 0.038 0.164 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.791 172.186 4250 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 11.28 % Favored : 88.21 % 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: 1.54 (0.28), residues: 913 helix: 2.22 (0.22), residues: 578 sheet: -1.87 (0.66), residues: 46 loop : -0.99 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 99 TYR 0.015 0.002 TYR G 39 PHE 0.027 0.002 PHE L 59 TRP 0.017 0.002 TRP K 82 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00626 (14357) covalent geometry : angle 0.62385 (20619) hydrogen bonds : bond 0.04932 ( 771) hydrogen bonds : angle 3.50100 ( 1940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.344 Fit side-chains REVERT: A 39 HIS cc_start: 0.7889 (t-90) cc_final: 0.7614 (t70) REVERT: A 73 GLU cc_start: 0.8857 (tt0) cc_final: 0.8506 (tt0) REVERT: A 115 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9210 (mmmm) REVERT: A 120 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (tpp) REVERT: A 125 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8658 (mm-40) REVERT: C 90 ASP cc_start: 0.8798 (t0) cc_final: 0.8570 (t0) REVERT: E 39 HIS cc_start: 0.8067 (t-90) cc_final: 0.7339 (m170) REVERT: E 56 LYS cc_start: 0.9570 (mtpp) cc_final: 0.9192 (mtmm) REVERT: E 59 GLU cc_start: 0.8779 (pp20) cc_final: 0.8316 (pp20) REVERT: F 23 ARG cc_start: 0.9326 (ppt170) cc_final: 0.9107 (pmt-80) REVERT: F 24 ASP cc_start: 0.9051 (p0) cc_final: 0.8819 (p0) REVERT: F 52 GLU cc_start: 0.8246 (mp0) cc_final: 0.7920 (pm20) REVERT: G 64 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8770 (tm-30) REVERT: G 73 ASN cc_start: 0.9626 (t0) cc_final: 0.9189 (t0) REVERT: K 52 PHE cc_start: 0.8670 (m-10) cc_final: 0.8367 (m-80) REVERT: K 53 LEU cc_start: 0.9375 (tt) cc_final: 0.8930 (mp) REVERT: K 78 ASN cc_start: 0.9522 (m-40) cc_final: 0.9272 (p0) REVERT: L 20 HIS cc_start: 0.5444 (m170) cc_final: 0.4546 (m-70) REVERT: L 59 PHE cc_start: 0.9302 (t80) cc_final: 0.8982 (t80) REVERT: L 77 PHE cc_start: 0.8332 (t80) cc_final: 0.7224 (t80) outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 0.1464 time to fit residues: 18.9112 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 113 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 ASN L 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.039350 restraints weight = 64960.095| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.90 r_work: 0.2551 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14357 Z= 0.188 Angle : 0.564 8.532 20619 Z= 0.328 Chirality : 0.035 0.171 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.598 175.463 4250 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.38 % Allowed : 11.79 % Favored : 87.83 % 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: 1.81 (0.28), residues: 913 helix: 2.45 (0.22), residues: 577 sheet: -2.02 (0.67), residues: 48 loop : -0.86 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.009 0.001 TYR B 88 PHE 0.012 0.001 PHE C 25 TRP 0.015 0.002 TRP K 82 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (14357) covalent geometry : angle 0.56443 (20619) hydrogen bonds : bond 0.04027 ( 771) hydrogen bonds : angle 3.20363 ( 1940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.382 Fit side-chains REVERT: A 39 HIS cc_start: 0.7882 (t-90) cc_final: 0.7499 (t70) REVERT: A 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8533 (tt0) REVERT: A 115 LYS cc_start: 0.9526 (mmmm) cc_final: 0.9197 (mmmm) REVERT: A 120 MET cc_start: 0.8712 (tpp) cc_final: 0.8445 (tpp) REVERT: A 125 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8725 (mm-40) REVERT: C 90 ASP cc_start: 0.8595 (t0) cc_final: 0.8301 (t0) REVERT: E 39 HIS cc_start: 0.8092 (t-90) cc_final: 0.7359 (m170) REVERT: E 56 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9164 (mtmm) REVERT: E 59 GLU cc_start: 0.8796 (pp20) cc_final: 0.8282 (pp20) REVERT: F 52 GLU cc_start: 0.8233 (mp0) cc_final: 0.7951 (pm20) REVERT: G 73 ASN cc_start: 0.9583 (t0) cc_final: 0.9136 (t0) REVERT: G 75 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9090 (mmmm) REVERT: K 1 MET cc_start: 0.3724 (ptp) cc_final: 0.3200 (pmm) REVERT: K 52 PHE cc_start: 0.8638 (m-10) cc_final: 0.8370 (m-80) REVERT: K 53 LEU cc_start: 0.9388 (tt) cc_final: 0.8871 (mp) REVERT: K 78 ASN cc_start: 0.9505 (m-40) cc_final: 0.9253 (p0) REVERT: L 20 HIS cc_start: 0.5378 (m170) cc_final: 0.4620 (m-70) REVERT: L 59 PHE cc_start: 0.9289 (t80) cc_final: 0.9003 (t80) REVERT: L 77 PHE cc_start: 0.8297 (t80) cc_final: 0.7157 (t80) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.1356 time to fit residues: 17.5122 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.061329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.039230 restraints weight = 65071.660| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.97 r_work: 0.2547 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14357 Z= 0.209 Angle : 0.571 8.668 20619 Z= 0.331 Chirality : 0.035 0.166 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.551 175.554 4250 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.38 % Allowed : 13.31 % Favored : 86.31 % 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: 1.98 (0.28), residues: 913 helix: 2.53 (0.22), residues: 577 sheet: -1.86 (0.68), residues: 50 loop : -0.66 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 76 TYR 0.008 0.001 TYR G 50 PHE 0.019 0.001 PHE C 25 TRP 0.016 0.002 TRP K 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00468 (14357) covalent geometry : angle 0.57077 (20619) hydrogen bonds : bond 0.04261 ( 771) hydrogen bonds : angle 3.20691 ( 1940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.226 Fit side-chains REVERT: A 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8524 (tt0) REVERT: A 115 LYS cc_start: 0.9524 (mmmm) cc_final: 0.9195 (mmmm) REVERT: A 120 MET cc_start: 0.8891 (tpp) cc_final: 0.8640 (tpp) REVERT: A 125 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8787 (mm-40) REVERT: C 90 ASP cc_start: 0.8584 (t0) cc_final: 0.8289 (t0) REVERT: E 39 HIS cc_start: 0.7705 (t-170) cc_final: 0.7298 (m170) REVERT: E 59 GLU cc_start: 0.8891 (pp20) cc_final: 0.8423 (pp20) REVERT: E 115 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9231 (mmtt) REVERT: G 64 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8801 (tm-30) REVERT: G 73 ASN cc_start: 0.9627 (t0) cc_final: 0.9153 (t0) REVERT: G 75 LYS cc_start: 0.9561 (mmmm) cc_final: 0.9120 (mmmm) REVERT: K 52 PHE cc_start: 0.8623 (m-10) cc_final: 0.8366 (m-80) REVERT: K 53 LEU cc_start: 0.9402 (tt) cc_final: 0.8885 (mp) REVERT: K 78 ASN cc_start: 0.9495 (m-40) cc_final: 0.9244 (p0) REVERT: L 20 HIS cc_start: 0.5268 (m170) cc_final: 0.4608 (m-70) REVERT: L 59 PHE cc_start: 0.9239 (t80) cc_final: 0.8826 (t80) REVERT: L 77 PHE cc_start: 0.8294 (t80) cc_final: 0.7119 (t80) outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 0.1379 time to fit residues: 17.3057 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 2.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.038859 restraints weight = 65324.145| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.91 r_work: 0.2538 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14357 Z= 0.233 Angle : 0.585 7.966 20619 Z= 0.338 Chirality : 0.036 0.159 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.541 170.095 4250 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 14.20 % Favored : 85.30 % 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: 2.02 (0.28), residues: 913 helix: 2.51 (0.22), residues: 579 sheet: -1.76 (0.75), residues: 44 loop : -0.59 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 76 TYR 0.009 0.001 TYR A 54 PHE 0.021 0.001 PHE C 25 TRP 0.015 0.002 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00521 (14357) covalent geometry : angle 0.58451 (20619) hydrogen bonds : bond 0.04374 ( 771) hydrogen bonds : angle 3.26389 ( 1940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.237 Fit side-chains REVERT: A 73 GLU cc_start: 0.8837 (tt0) cc_final: 0.8522 (tt0) REVERT: A 115 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9188 (mmmm) REVERT: A 120 MET cc_start: 0.8903 (tpp) cc_final: 0.8664 (tpp) REVERT: A 125 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8802 (mm-40) REVERT: C 90 ASP cc_start: 0.8638 (t0) cc_final: 0.8335 (t0) REVERT: D 30 ARG cc_start: 0.7572 (ptt180) cc_final: 0.7327 (ptt180) REVERT: E 59 GLU cc_start: 0.9134 (pp20) cc_final: 0.8617 (pp20) REVERT: E 115 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9272 (mmtt) REVERT: F 52 GLU cc_start: 0.8352 (mp0) cc_final: 0.8115 (pm20) REVERT: G 64 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8708 (tm-30) REVERT: K 52 PHE cc_start: 0.8648 (m-10) cc_final: 0.8380 (m-80) REVERT: K 53 LEU cc_start: 0.9425 (tt) cc_final: 0.8904 (mp) REVERT: K 78 ASN cc_start: 0.9510 (m-40) cc_final: 0.9278 (p0) REVERT: L 20 HIS cc_start: 0.5166 (m170) cc_final: 0.4654 (m-70) REVERT: L 52 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6817 (t80) REVERT: L 59 PHE cc_start: 0.9156 (t80) cc_final: 0.8831 (t80) REVERT: L 61 TYR cc_start: 0.7414 (t80) cc_final: 0.7080 (t80) REVERT: L 77 PHE cc_start: 0.8242 (t80) cc_final: 0.7013 (t80) outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 0.1553 time to fit residues: 19.1418 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 52 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.038973 restraints weight = 64919.994| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.90 r_work: 0.2544 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14357 Z= 0.213 Angle : 0.578 8.753 20619 Z= 0.334 Chirality : 0.035 0.156 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.472 171.184 4250 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.76 % Allowed : 14.45 % Favored : 84.79 % 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: 2.06 (0.28), residues: 913 helix: 2.50 (0.22), residues: 583 sheet: -1.44 (0.78), residues: 43 loop : -0.60 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 76 TYR 0.008 0.001 TYR C 50 PHE 0.017 0.001 PHE C 25 TRP 0.015 0.002 TRP K 82 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00478 (14357) covalent geometry : angle 0.57807 (20619) hydrogen bonds : bond 0.04197 ( 771) hydrogen bonds : angle 3.19117 ( 1940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.443 Fit side-chains REVERT: A 73 GLU cc_start: 0.8829 (tt0) cc_final: 0.8517 (tt0) REVERT: A 115 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9177 (mmmm) REVERT: A 120 MET cc_start: 0.8883 (tpp) cc_final: 0.8648 (tpp) REVERT: A 125 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8825 (mm-40) REVERT: C 90 ASP cc_start: 0.8586 (t0) cc_final: 0.8260 (t0) REVERT: D 30 ARG cc_start: 0.7687 (ptt180) cc_final: 0.7417 (ptt180) REVERT: E 39 HIS cc_start: 0.7497 (t-170) cc_final: 0.7071 (m170) REVERT: E 59 GLU cc_start: 0.9173 (pp20) cc_final: 0.8571 (pp20) REVERT: E 115 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9263 (mmtt) REVERT: F 52 GLU cc_start: 0.8273 (mp0) cc_final: 0.7914 (pm20) REVERT: G 64 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8738 (tm-30) REVERT: G 73 ASN cc_start: 0.9556 (t0) cc_final: 0.9204 (t0) REVERT: K 52 PHE cc_start: 0.8662 (m-10) cc_final: 0.8392 (m-80) REVERT: K 53 LEU cc_start: 0.9427 (tt) cc_final: 0.8907 (mp) REVERT: K 78 ASN cc_start: 0.9516 (m-40) cc_final: 0.9292 (p0) REVERT: L 20 HIS cc_start: 0.5190 (m170) cc_final: 0.4691 (m-70) REVERT: L 52 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7805 (t80) REVERT: L 59 PHE cc_start: 0.9225 (t80) cc_final: 0.8903 (t80) REVERT: L 61 TYR cc_start: 0.7328 (t80) cc_final: 0.7120 (t80) REVERT: L 77 PHE cc_start: 0.8271 (t80) cc_final: 0.7010 (t80) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.1518 time to fit residues: 19.8522 Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain L residue 52 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.060638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.038640 restraints weight = 65256.622| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.91 r_work: 0.2528 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14357 Z= 0.243 Angle : 0.606 8.693 20619 Z= 0.348 Chirality : 0.036 0.156 2322 Planarity : 0.004 0.045 1605 Dihedral : 30.539 170.640 4250 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.76 % Allowed : 14.58 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.97 (0.28), residues: 913 helix: 2.43 (0.22), residues: 580 sheet: -1.56 (0.75), residues: 43 loop : -0.59 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.009 0.001 TYR C 50 PHE 0.020 0.002 PHE C 25 TRP 0.017 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00545 (14357) covalent geometry : angle 0.60580 (20619) hydrogen bonds : bond 0.04561 ( 771) hydrogen bonds : angle 3.38958 ( 1940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8821 (tt0) cc_final: 0.8506 (tt0) REVERT: A 115 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9167 (mmmm) REVERT: A 120 MET cc_start: 0.8923 (tpp) cc_final: 0.8700 (tpp) REVERT: A 125 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8810 (mm-40) REVERT: C 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8345 (t0) REVERT: D 30 ARG cc_start: 0.7891 (ptt180) cc_final: 0.7630 (ptt180) REVERT: D 56 MET cc_start: 0.9344 (tpp) cc_final: 0.8376 (tpp) REVERT: E 59 GLU cc_start: 0.9095 (pp20) cc_final: 0.8558 (pp20) REVERT: E 115 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9253 (mmtt) REVERT: F 52 GLU cc_start: 0.8357 (mp0) cc_final: 0.7983 (pm20) REVERT: G 64 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8740 (tm-30) REVERT: G 73 ASN cc_start: 0.9467 (t0) cc_final: 0.9098 (t0) REVERT: K 52 PHE cc_start: 0.8670 (m-10) cc_final: 0.8399 (m-80) REVERT: K 53 LEU cc_start: 0.9438 (tt) cc_final: 0.8839 (mp) REVERT: K 78 ASN cc_start: 0.9533 (m-40) cc_final: 0.9327 (p0) REVERT: L 20 HIS cc_start: 0.5222 (m170) cc_final: 0.4992 (m-70) REVERT: L 52 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7723 (t80) REVERT: L 77 PHE cc_start: 0.8435 (t80) cc_final: 0.7073 (t80) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.1538 time to fit residues: 20.1296 Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain L residue 52 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.060833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.038815 restraints weight = 64873.426| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.87 r_work: 0.2538 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14357 Z= 0.226 Angle : 0.604 9.138 20619 Z= 0.346 Chirality : 0.036 0.150 2322 Planarity : 0.004 0.063 1605 Dihedral : 30.460 171.075 4250 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.63 % Allowed : 15.08 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.03 (0.28), residues: 913 helix: 2.46 (0.22), residues: 580 sheet: -1.55 (0.76), residues: 45 loop : -0.49 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 76 TYR 0.008 0.001 TYR C 50 PHE 0.018 0.001 PHE C 25 TRP 0.018 0.002 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00508 (14357) covalent geometry : angle 0.60414 (20619) hydrogen bonds : bond 0.04253 ( 771) hydrogen bonds : angle 3.28833 ( 1940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.377 Fit side-chains REVERT: A 73 GLU cc_start: 0.8823 (tt0) cc_final: 0.8513 (tt0) REVERT: A 115 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9220 (mmmm) REVERT: A 120 MET cc_start: 0.8908 (tpp) cc_final: 0.8677 (tpp) REVERT: C 90 ASP cc_start: 0.8633 (t0) cc_final: 0.8298 (t0) REVERT: D 30 ARG cc_start: 0.7930 (ptt180) cc_final: 0.7670 (ptt180) REVERT: E 39 HIS cc_start: 0.7487 (t-170) cc_final: 0.7143 (m170) REVERT: E 59 GLU cc_start: 0.9119 (pp20) cc_final: 0.8559 (pp20) REVERT: E 115 LYS cc_start: 0.9567 (mmmm) cc_final: 0.9257 (mmtt) REVERT: F 52 GLU cc_start: 0.8230 (mp0) cc_final: 0.7945 (pm20) REVERT: G 64 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8713 (tm-30) REVERT: G 73 ASN cc_start: 0.9498 (t0) cc_final: 0.9118 (t0) REVERT: K 52 PHE cc_start: 0.8685 (m-10) cc_final: 0.8333 (m-80) REVERT: K 78 ASN cc_start: 0.9517 (m-40) cc_final: 0.9305 (p0) REVERT: L 20 HIS cc_start: 0.5270 (m170) cc_final: 0.4786 (m-70) REVERT: L 52 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7692 (t80) REVERT: L 59 PHE cc_start: 0.9216 (t80) cc_final: 0.8914 (t80) REVERT: L 61 TYR cc_start: 0.7243 (t80) cc_final: 0.6878 (t80) REVERT: L 77 PHE cc_start: 0.8479 (t80) cc_final: 0.7120 (t80) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.1383 time to fit residues: 18.1851 Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain L residue 52 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.061282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.039094 restraints weight = 65285.284| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.94 r_work: 0.2552 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14357 Z= 0.187 Angle : 0.593 9.547 20619 Z= 0.339 Chirality : 0.035 0.151 2322 Planarity : 0.004 0.056 1605 Dihedral : 30.429 171.564 4250 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.63 % Allowed : 15.08 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.14 (0.28), residues: 913 helix: 2.54 (0.22), residues: 580 sheet: -1.52 (0.76), residues: 45 loop : -0.44 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 76 TYR 0.007 0.001 TYR C 50 PHE 0.015 0.001 PHE C 25 TRP 0.018 0.002 TRP K 82 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00420 (14357) covalent geometry : angle 0.59296 (20619) hydrogen bonds : bond 0.04040 ( 771) hydrogen bonds : angle 3.19611 ( 1940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.62 seconds wall clock time: 58 minutes 38.66 seconds (3518.66 seconds total)