Starting phenix.real_space_refine on Thu May 15 14:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pep_17634/05_2025/8pep_17634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pep_17634/05_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_17634/05_2025/8pep_17634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pep_17634/05_2025/8pep_17634.map" model { file = "/net/cci-nas-00/data/ceres_data/8pep_17634/05_2025/8pep_17634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pep_17634/05_2025/8pep_17634.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.46, per 1000 atoms: 0.55 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: 3.08 Conformation dependent library (CDL) restraints added in 986.0 milliseconds 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: 6.20 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: 4.68 Time building geometry restraints manager: 3.65 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.950 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (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 TRP 0.008 0.001 TRP K 21 HIS 0.007 0.001 HIS L 20 PHE 0.036 0.002 PHE C 25 TYR 0.035 0.002 TYR K 61 ARG 0.022 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.19360 ( 771) hydrogen bonds : angle 6.29768 ( 1940) covalent geometry : bond 0.00381 (14357) covalent geometry : angle 0.71631 (20619) *********************** 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 : 1.089 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: 0.3810 time to fit residues: 77.0323 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 : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.062960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041114 restraints weight = 65225.067| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.92 r_work: 0.2612 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2249 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= 0.185 Angle : 0.603 9.237 20619 Z= 0.349 Chirality : 0.037 0.194 2322 Planarity : 0.005 0.042 1605 Dihedral : 31.239 179.239 4250 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 913 helix: 2.20 (0.22), residues: 562 sheet: -2.64 (0.67), residues: 42 loop : -0.93 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 82 HIS 0.007 0.001 HIS G 31 PHE 0.014 0.001 PHE C 25 TYR 0.031 0.002 TYR L 61 ARG 0.018 0.001 ARG K 74 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 771) hydrogen bonds : angle 3.36647 ( 1940) covalent geometry : bond 0.00409 (14357) covalent geometry : angle 0.60255 (20619) *********************** 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 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8868 (tt0) cc_final: 0.8551 (tt0) REVERT: C 92 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 30 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7849 (ptt-90) REVERT: E 56 LYS cc_start: 0.9499 (mtpp) cc_final: 0.9078 (mtmm) REVERT: F 52 GLU cc_start: 0.8148 (mp0) cc_final: 0.7940 (pm20) REVERT: G 64 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8747 (tm-30) REVERT: G 73 ASN cc_start: 0.9536 (t0) cc_final: 0.9161 (t0) REVERT: G 104 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8878 (mm-40) REVERT: H 30 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8280 (ptt90) REVERT: K 1 MET cc_start: 0.2453 (ptp) cc_final: 0.1588 (pmm) REVERT: K 52 PHE cc_start: 0.8620 (m-10) cc_final: 0.8321 (m-80) REVERT: K 53 LEU cc_start: 0.9161 (tt) cc_final: 0.8886 (mp) REVERT: K 78 ASN cc_start: 0.9460 (m-40) cc_final: 0.9206 (p0) REVERT: L 40 LEU cc_start: 0.7506 (tp) cc_final: 0.7115 (tt) REVERT: L 77 PHE cc_start: 0.8191 (t80) cc_final: 0.7565 (t80) REVERT: L 78 ASN cc_start: 0.9021 (m-40) cc_final: 0.8615 (m-40) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.3105 time to fit residues: 45.0793 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 81 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.063254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041442 restraints weight = 65252.139| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.92 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: 0.8954 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14357 Z= 0.160 Angle : 0.550 7.226 20619 Z= 0.323 Chirality : 0.035 0.182 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.756 170.255 4250 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.25 % Allowed : 10.01 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.28), residues: 913 helix: 2.50 (0.22), residues: 561 sheet: -2.08 (0.68), residues: 45 loop : -0.95 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 82 HIS 0.006 0.001 HIS L 20 PHE 0.009 0.001 PHE K 5 TYR 0.012 0.001 TYR L 61 ARG 0.008 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 771) hydrogen bonds : angle 3.16127 ( 1940) covalent geometry : bond 0.00349 (14357) covalent geometry : angle 0.55038 (20619) *********************** 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 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.098 Fit side-chains REVERT: A 73 GLU cc_start: 0.8830 (tt0) cc_final: 0.8503 (tt0) REVERT: A 120 MET cc_start: 0.8658 (tpp) cc_final: 0.8414 (tpp) REVERT: A 125 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8657 (mm-40) REVERT: C 90 ASP cc_start: 0.8394 (t0) cc_final: 0.8185 (t0) REVERT: D 76 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8377 (ttm110) REVERT: E 39 HIS cc_start: 0.7568 (t-90) cc_final: 0.6965 (m170) REVERT: E 56 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9178 (mtmm) REVERT: G 73 ASN cc_start: 0.9583 (t0) cc_final: 0.9150 (t0) REVERT: K 1 MET cc_start: 0.4057 (ptp) cc_final: 0.3299 (pmm) REVERT: K 52 PHE cc_start: 0.8620 (m-10) cc_final: 0.8275 (m-80) REVERT: K 78 ASN cc_start: 0.9457 (m-40) cc_final: 0.8943 (p0) REVERT: K 79 GLU cc_start: 0.9504 (pt0) cc_final: 0.9148 (pm20) REVERT: L 20 HIS cc_start: 0.5840 (m170) cc_final: 0.5302 (m-70) REVERT: L 77 PHE cc_start: 0.8645 (t80) cc_final: 0.7731 (t80) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.3271 time to fit residues: 43.5299 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** 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 = 0.3540 r_free = 0.3540 target = 0.063284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041411 restraints weight = 64596.927| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.93 r_work: 0.2623 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14357 Z= 0.157 Angle : 0.534 9.108 20619 Z= 0.313 Chirality : 0.034 0.164 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.547 166.632 4250 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.13 % Allowed : 10.39 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.28), residues: 913 helix: 2.55 (0.22), residues: 576 sheet: -2.09 (0.63), residues: 52 loop : -0.90 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.028 0.001 PHE L 59 TYR 0.008 0.001 TYR G 50 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 771) hydrogen bonds : angle 3.03783 ( 1940) covalent geometry : bond 0.00347 (14357) covalent geometry : angle 0.53385 (20619) *********************** 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 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 1.076 Fit side-chains REVERT: A 73 GLU cc_start: 0.8876 (tt0) cc_final: 0.8556 (tt0) REVERT: C 90 ASP cc_start: 0.8414 (t0) cc_final: 0.8180 (t0) REVERT: D 56 MET cc_start: 0.9179 (tpp) cc_final: 0.8528 (tpp) REVERT: D 76 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8396 (ttm110) REVERT: E 39 HIS cc_start: 0.7527 (t-90) cc_final: 0.6979 (m170) REVERT: E 56 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9159 (mtmm) REVERT: G 64 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8807 (tm-30) REVERT: G 73 ASN cc_start: 0.9641 (t0) cc_final: 0.9244 (t0) REVERT: K 52 PHE cc_start: 0.8619 (m-10) cc_final: 0.8332 (m-80) REVERT: K 53 LEU cc_start: 0.9340 (tt) cc_final: 0.8925 (mp) REVERT: K 78 ASN cc_start: 0.9464 (m-40) cc_final: 0.8973 (p0) REVERT: K 79 GLU cc_start: 0.9491 (pt0) cc_final: 0.9098 (pm20) REVERT: L 20 HIS cc_start: 0.5395 (m170) cc_final: 0.4573 (m-70) REVERT: L 59 PHE cc_start: 0.9321 (t80) cc_final: 0.9006 (t80) REVERT: L 77 PHE cc_start: 0.8595 (t80) cc_final: 0.7512 (t80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.3316 time to fit residues: 43.3578 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 : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 72 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.037229 restraints weight = 66352.510| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.00 r_work: 0.2486 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 14357 Z= 0.396 Angle : 0.711 8.042 20619 Z= 0.403 Chirality : 0.043 0.170 2322 Planarity : 0.005 0.042 1605 Dihedral : 30.903 177.080 4250 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.51 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 913 helix: 1.99 (0.21), residues: 577 sheet: -2.09 (0.63), residues: 53 loop : -1.00 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 82 HIS 0.007 0.001 HIS B 75 PHE 0.039 0.002 PHE C 25 TYR 0.020 0.002 TYR G 39 ARG 0.005 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 771) hydrogen bonds : angle 3.79972 ( 1940) covalent geometry : bond 0.00893 (14357) covalent geometry : angle 0.71083 (20619) *********************** 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 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.132 Fit side-chains REVERT: A 115 LYS cc_start: 0.9544 (mmmm) cc_final: 0.9229 (mmmm) REVERT: A 125 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8750 (mm-40) REVERT: C 36 LYS cc_start: 0.9549 (mtpp) cc_final: 0.9325 (ttmm) REVERT: D 56 MET cc_start: 0.9271 (tpp) cc_final: 0.9063 (tpp) REVERT: E 59 GLU cc_start: 0.8717 (pp20) cc_final: 0.8247 (pp20) REVERT: E 105 GLU cc_start: 0.7882 (pp20) cc_final: 0.7395 (pp20) REVERT: E 115 LYS cc_start: 0.9607 (mmmm) cc_final: 0.9289 (mmtt) REVERT: F 23 ARG cc_start: 0.9371 (ppt170) cc_final: 0.9099 (pmt-80) REVERT: G 64 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8993 (tm-30) REVERT: G 72 ASP cc_start: 0.8961 (m-30) cc_final: 0.8732 (m-30) REVERT: K 52 PHE cc_start: 0.8650 (m-10) cc_final: 0.8298 (m-80) REVERT: K 78 ASN cc_start: 0.9536 (m-40) cc_final: 0.9305 (p0) REVERT: L 20 HIS cc_start: 0.5267 (m170) cc_final: 0.4542 (m-70) REVERT: L 59 PHE cc_start: 0.9128 (t80) cc_final: 0.8725 (t80) REVERT: L 77 PHE cc_start: 0.8185 (t80) cc_final: 0.7023 (t80) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.3289 time to fit residues: 40.5647 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 : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.039790 restraints weight = 65667.597| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.98 r_work: 0.2571 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14357 Z= 0.159 Angle : 0.564 8.585 20619 Z= 0.327 Chirality : 0.035 0.164 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.549 179.208 4250 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.51 % Allowed : 13.05 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.28), residues: 913 helix: 2.47 (0.22), residues: 578 sheet: -1.80 (0.72), residues: 50 loop : -0.79 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 82 HIS 0.006 0.001 HIS F 75 PHE 0.009 0.001 PHE K 5 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 771) hydrogen bonds : angle 3.07637 ( 1940) covalent geometry : bond 0.00353 (14357) covalent geometry : angle 0.56424 (20619) *********************** 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 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.239 Fit side-chains REVERT: A 73 GLU cc_start: 0.9090 (tt0) cc_final: 0.8826 (tt0) REVERT: A 115 LYS cc_start: 0.9525 (mmmm) cc_final: 0.9193 (mmmm) REVERT: D 56 MET cc_start: 0.9249 (tpp) cc_final: 0.8169 (tpp) REVERT: E 39 HIS cc_start: 0.7374 (t-170) cc_final: 0.6962 (m170) REVERT: E 59 GLU cc_start: 0.8824 (pp20) cc_final: 0.8314 (pp20) REVERT: E 115 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9278 (mmtt) REVERT: G 72 ASP cc_start: 0.8980 (m-30) cc_final: 0.8706 (m-30) REVERT: G 73 ASN cc_start: 0.9600 (t0) cc_final: 0.9226 (t0) REVERT: K 1 MET cc_start: 0.3624 (ptp) cc_final: 0.3233 (pmm) REVERT: K 52 PHE cc_start: 0.8652 (m-10) cc_final: 0.8368 (m-80) REVERT: K 53 LEU cc_start: 0.9255 (tt) cc_final: 0.8753 (mp) REVERT: K 78 ASN cc_start: 0.9524 (m-40) cc_final: 0.9276 (p0) REVERT: L 20 HIS cc_start: 0.5288 (m170) cc_final: 0.4597 (m-70) REVERT: L 59 PHE cc_start: 0.9209 (t80) cc_final: 0.8802 (t80) REVERT: L 77 PHE cc_start: 0.8446 (t80) cc_final: 0.7216 (t80) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.3066 time to fit residues: 40.7984 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.062296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040125 restraints weight = 65064.425| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.95 r_work: 0.2578 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14357 Z= 0.166 Angle : 0.560 9.584 20619 Z= 0.323 Chirality : 0.034 0.151 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.462 174.898 4250 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.63 % Allowed : 13.43 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.28), residues: 913 helix: 2.70 (0.22), residues: 577 sheet: -1.69 (0.70), residues: 50 loop : -0.57 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 82 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE C 25 TYR 0.009 0.001 TYR F 51 ARG 0.014 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 771) hydrogen bonds : angle 3.02202 ( 1940) covalent geometry : bond 0.00370 (14357) covalent geometry : angle 0.56004 (20619) *********************** 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 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.111 Fit side-chains REVERT: A 73 GLU cc_start: 0.8976 (tt0) cc_final: 0.8607 (tt0) REVERT: A 115 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9221 (mmmm) REVERT: D 56 MET cc_start: 0.9163 (tpp) cc_final: 0.8614 (tpp) REVERT: D 76 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8397 (ttm110) REVERT: E 59 GLU cc_start: 0.8847 (pp20) cc_final: 0.8342 (pp20) REVERT: E 115 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9229 (mmtt) REVERT: G 64 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8803 (tm-30) REVERT: G 72 ASP cc_start: 0.9004 (m-30) cc_final: 0.8723 (m-30) REVERT: G 73 ASN cc_start: 0.9615 (t0) cc_final: 0.9231 (t0) REVERT: K 52 PHE cc_start: 0.8654 (m-10) cc_final: 0.8379 (m-80) REVERT: K 53 LEU cc_start: 0.9407 (tt) cc_final: 0.8828 (mp) REVERT: K 78 ASN cc_start: 0.9506 (m-40) cc_final: 0.9251 (p0) REVERT: L 20 HIS cc_start: 0.5223 (m170) cc_final: 0.4576 (m-70) REVERT: L 52 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7817 (t80) REVERT: L 59 PHE cc_start: 0.9279 (t80) cc_final: 0.8925 (t80) REVERT: L 61 TYR cc_start: 0.7345 (t80) cc_final: 0.7052 (t80) REVERT: L 77 PHE cc_start: 0.8410 (t80) cc_final: 0.7184 (t80) outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.3067 time to fit residues: 39.0271 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 47 THR 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 79 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.038432 restraints weight = 65670.481| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.89 r_work: 0.2525 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14357 Z= 0.261 Angle : 0.616 8.208 20619 Z= 0.352 Chirality : 0.037 0.159 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.550 168.837 4250 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.76 % Allowed : 14.07 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 913 helix: 2.43 (0.22), residues: 582 sheet: -1.34 (0.82), residues: 43 loop : -0.65 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 82 HIS 0.004 0.001 HIS D 79 PHE 0.027 0.002 PHE C 25 TYR 0.011 0.002 TYR F 51 ARG 0.012 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 771) hydrogen bonds : angle 3.34305 ( 1940) covalent geometry : bond 0.00586 (14357) covalent geometry : angle 0.61612 (20619) *********************** 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 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.158 Fit side-chains REVERT: A 115 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9165 (mmmm) REVERT: D 56 MET cc_start: 0.9259 (tpp) cc_final: 0.8671 (tpp) REVERT: E 39 HIS cc_start: 0.7703 (t-170) cc_final: 0.7002 (m170) REVERT: E 59 GLU cc_start: 0.9073 (pp20) cc_final: 0.8649 (pp20) REVERT: E 115 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9269 (mmtt) REVERT: F 23 ARG cc_start: 0.9385 (ppt170) cc_final: 0.9059 (pmt-80) REVERT: F 24 ASP cc_start: 0.9154 (p0) cc_final: 0.8830 (p0) REVERT: G 64 GLU cc_start: 0.9210 (tm-30) cc_final: 0.9005 (tm-30) REVERT: G 72 ASP cc_start: 0.8960 (m-30) cc_final: 0.8650 (m-30) REVERT: K 52 PHE cc_start: 0.8641 (m-10) cc_final: 0.8372 (m-80) REVERT: K 53 LEU cc_start: 0.9320 (tt) cc_final: 0.8813 (mp) REVERT: K 78 ASN cc_start: 0.9533 (m-40) cc_final: 0.9296 (p0) REVERT: L 20 HIS cc_start: 0.5193 (m170) cc_final: 0.4698 (m-70) REVERT: L 52 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7831 (t80) REVERT: L 59 PHE cc_start: 0.9216 (t80) cc_final: 0.8903 (t80) REVERT: L 61 TYR cc_start: 0.7279 (t80) cc_final: 0.6991 (t80) REVERT: L 77 PHE cc_start: 0.8416 (t80) cc_final: 0.7133 (t80) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 0.3115 time to fit residues: 39.2721 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 47 THR 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 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.062015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.039928 restraints weight = 63736.446| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.93 r_work: 0.2575 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14357 Z= 0.160 Angle : 0.570 10.452 20619 Z= 0.328 Chirality : 0.034 0.154 2322 Planarity : 0.004 0.054 1605 Dihedral : 30.392 171.911 4250 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 14.45 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.28), residues: 913 helix: 2.58 (0.22), residues: 583 sheet: -1.35 (0.81), residues: 43 loop : -0.54 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 82 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE L 52 TYR 0.009 0.001 TYR F 51 ARG 0.014 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 771) hydrogen bonds : angle 3.01961 ( 1940) covalent geometry : bond 0.00356 (14357) covalent geometry : angle 0.57026 (20619) *********************** 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 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 1.074 Fit side-chains REVERT: A 39 HIS cc_start: 0.8319 (t-90) cc_final: 0.8115 (t-90) REVERT: A 115 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9172 (mmmm) REVERT: D 56 MET cc_start: 0.9241 (tpp) cc_final: 0.8110 (tpp) REVERT: D 76 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8423 (ttm110) REVERT: E 39 HIS cc_start: 0.7630 (t-170) cc_final: 0.6953 (m170) REVERT: E 59 GLU cc_start: 0.9101 (pp20) cc_final: 0.8660 (pp20) REVERT: E 115 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9259 (mmtt) REVERT: G 64 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8745 (tm-30) REVERT: G 72 ASP cc_start: 0.8977 (m-30) cc_final: 0.8694 (m-30) REVERT: G 73 ASN cc_start: 0.9564 (t0) cc_final: 0.9250 (t0) REVERT: K 52 PHE cc_start: 0.8641 (m-10) cc_final: 0.8399 (m-80) REVERT: K 53 LEU cc_start: 0.9414 (tt) cc_final: 0.8808 (mp) REVERT: K 78 ASN cc_start: 0.9501 (m-40) cc_final: 0.9246 (p0) REVERT: L 20 HIS cc_start: 0.5225 (m170) cc_final: 0.4718 (m-70) REVERT: L 52 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7801 (t80) REVERT: L 59 PHE cc_start: 0.9214 (t80) cc_final: 0.8901 (t80) REVERT: L 77 PHE cc_start: 0.8433 (t80) cc_final: 0.7107 (t80) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.3109 time to fit residues: 40.8083 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 47 THR 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 33 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.062927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.040819 restraints weight = 64534.487| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.91 r_work: 0.2606 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14357 Z= 0.154 Angle : 0.567 10.750 20619 Z= 0.324 Chirality : 0.034 0.201 2322 Planarity : 0.004 0.058 1605 Dihedral : 30.284 173.504 4250 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.51 % Allowed : 14.45 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.28), residues: 913 helix: 2.70 (0.21), residues: 583 sheet: -1.40 (0.82), residues: 43 loop : -0.47 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.007 0.001 TYR H 37 ARG 0.014 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 771) hydrogen bonds : angle 2.96362 ( 1940) covalent geometry : bond 0.00343 (14357) covalent geometry : angle 0.56746 (20619) ********************** 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 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.016 Fit side-chains REVERT: A 115 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9168 (mmmm) REVERT: D 56 MET cc_start: 0.9144 (tpp) cc_final: 0.8534 (tpp) REVERT: E 59 GLU cc_start: 0.9102 (pp20) cc_final: 0.8638 (pp20) REVERT: E 115 LYS cc_start: 0.9593 (mmmm) cc_final: 0.9285 (mmtt) REVERT: G 64 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8792 (tm-30) REVERT: G 72 ASP cc_start: 0.8989 (m-30) cc_final: 0.8696 (m-30) REVERT: G 73 ASN cc_start: 0.9514 (t0) cc_final: 0.9191 (t0) REVERT: K 52 PHE cc_start: 0.8652 (m-10) cc_final: 0.8385 (m-80) REVERT: K 53 LEU cc_start: 0.9370 (tt) cc_final: 0.8719 (mp) REVERT: K 78 ASN cc_start: 0.9483 (m-40) cc_final: 0.9225 (p0) REVERT: L 20 HIS cc_start: 0.5372 (m170) cc_final: 0.4709 (m-70) REVERT: L 40 LEU cc_start: 0.7950 (tt) cc_final: 0.7664 (tt) REVERT: L 52 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7759 (t80) REVERT: L 59 PHE cc_start: 0.9259 (t80) cc_final: 0.8902 (t80) REVERT: L 77 PHE cc_start: 0.8462 (t80) cc_final: 0.7108 (t80) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.3129 time to fit residues: 39.8720 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain L residue 47 THR 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 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 111 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.063237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.041275 restraints weight = 64871.355| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.90 r_work: 0.2613 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14357 Z= 0.153 Angle : 0.565 10.611 20619 Z= 0.321 Chirality : 0.034 0.146 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.209 173.457 4250 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.51 % Allowed : 14.58 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.28), residues: 913 helix: 2.84 (0.22), residues: 578 sheet: -1.57 (0.83), residues: 41 loop : -0.31 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.008 0.001 PHE C 25 TYR 0.018 0.001 TYR L 61 ARG 0.008 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 771) hydrogen bonds : angle 2.89570 ( 1940) covalent geometry : bond 0.00340 (14357) covalent geometry : angle 0.56465 (20619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7061.70 seconds wall clock time: 122 minutes 28.54 seconds (7348.54 seconds total)