Starting phenix.real_space_refine on Sat Oct 11 05:44:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc6_19049/10_2025/8rc6_19049.map" } resolution = 3.3 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= 0.000 sd= 0.000 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 S 18 5.16 5 C 3932 2.51 5 N 1002 2.21 5 O 1166 1.98 5 H 6076 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12194 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2019 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "B" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2034 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "C" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2019 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "D" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2044 Classifications: {'peptide': 131} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "E" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2044 Classifications: {'peptide': 131} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2034 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Time building chain proxies: 2.12, per 1000 atoms: 0.17 Number of scatterers: 12194 At special positions: 0 Unit cell: (60.507, 96.957, 103.518, 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 18 16.00 O 1166 8.00 N 1002 7.00 C 3932 6.00 H 6076 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 365.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 50.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.584A pdb=" N TYR A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.750A pdb=" N ARG A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.565A pdb=" N THR B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.767A pdb=" N ASP B 47 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 48 " --> pdb=" O PRO B 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 48' Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.843A pdb=" N ARG B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.848A pdb=" N SER C 41 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.707A pdb=" N GLU C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 112 through 125 removed outlier: 4.423A pdb=" N ASN C 116 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 28 removed outlier: 4.194A pdb=" N LYS D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 111 through 125 removed outlier: 4.028A pdb=" N ASN D 116 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 56 through 64 removed outlier: 3.910A pdb=" N ALA E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 92 through 106 removed outlier: 4.071A pdb=" N TYR E 104 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 126 removed outlier: 4.155A pdb=" N ASN E 116 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 28 removed outlier: 4.115A pdb=" N TYR F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 64 through 74 removed outlier: 3.885A pdb=" N THR F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.875A pdb=" N GLU F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.466A pdb=" N TYR B 84 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL C 86 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 86 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 34 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 111 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.210A pdb=" N VAL D 34 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 87 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR D 36 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR D 84 " --> pdb=" O TYR E 84 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL E 86 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 86 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 34 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU E 87 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR E 36 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AA9, first strand: chain 'E' and resid 107 through 108 291 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6070 1.03 - 1.22: 6 1.22 - 1.42: 2656 1.42 - 1.61: 3576 1.61 - 1.80: 30 Bond restraints: 12338 Sorted by residual: bond pdb=" N ALA D 3 " pdb=" H1 ALA D 3 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ALA E 3 " pdb=" H1 ALA E 3 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C VAL F 86 " pdb=" N LEU F 87 " ideal model delta sigma weight residual 1.323 1.299 0.023 1.64e-02 3.72e+03 2.02e+00 bond pdb=" C GLY D 52 " pdb=" O GLY D 52 " ideal model delta sigma weight residual 1.243 1.232 0.011 9.30e-03 1.16e+04 1.28e+00 bond pdb=" CA ILE A 76 " pdb=" CB ILE A 76 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.31e-02 5.83e+03 1.10e+00 ... (remaining 12333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 21201 1.21 - 2.41: 1001 2.41 - 3.62: 49 3.62 - 4.83: 10 4.83 - 6.04: 5 Bond angle restraints: 22266 Sorted by residual: angle pdb=" N ILE B 114 " pdb=" CA ILE B 114 " pdb=" C ILE B 114 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N ILE B 44 " pdb=" CA ILE B 44 " pdb=" C ILE B 44 " ideal model delta sigma weight residual 108.88 114.14 -5.26 2.16e+00 2.14e-01 5.93e+00 angle pdb=" CA ILE B 114 " pdb=" C ILE B 114 " pdb=" N LEU B 115 " ideal model delta sigma weight residual 119.87 116.85 3.02 1.34e+00 5.57e-01 5.07e+00 angle pdb=" N TYR E 39 " pdb=" CA TYR E 39 " pdb=" C TYR E 39 " ideal model delta sigma weight residual 111.28 113.66 -2.38 1.09e+00 8.42e-01 4.76e+00 angle pdb=" CA ALA E 3 " pdb=" N ALA E 3 " pdb=" H1 ALA E 3 " ideal model delta sigma weight residual 120.00 113.96 6.04 3.00e+00 1.11e-01 4.05e+00 ... (remaining 22261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 5376 16.66 - 33.32: 367 33.32 - 49.98: 97 49.98 - 66.64: 37 66.64 - 83.30: 9 Dihedral angle restraints: 5886 sinusoidal: 3138 harmonic: 2748 Sorted by residual: dihedral pdb=" CA SER E 38 " pdb=" C SER E 38 " pdb=" N TYR E 39 " pdb=" CA TYR E 39 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP A 10 " pdb=" C TRP A 10 " pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LYS D 9 " pdb=" C LYS D 9 " pdb=" N TRP D 10 " pdb=" CA TRP D 10 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 596 0.031 - 0.061: 256 0.061 - 0.092: 85 0.092 - 0.122: 43 0.122 - 0.153: 10 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE E 44 " pdb=" N ILE E 44 " pdb=" C ILE E 44 " pdb=" CB ILE E 44 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 987 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 48 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO E 49 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 87 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO F 88 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 78 " 0.016 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO D 79 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " 0.014 5.00e-02 4.00e+02 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 492 2.16 - 2.77: 24163 2.77 - 3.38: 35164 3.38 - 3.99: 44772 3.99 - 4.60: 70729 Nonbonded interactions: 175320 Sorted by model distance: nonbonded pdb=" O LYS A 29 " pdb=" HE2 HIS A 56 " model vdw 1.544 2.450 nonbonded pdb="HD21 ASN A 80 " pdb=" OD1 ASN F 78 " model vdw 1.566 2.450 nonbonded pdb=" OD1 ASN C 78 " pdb=" H ASN C 80 " model vdw 1.577 2.450 nonbonded pdb=" O LEU E 24 " pdb=" H ASN E 27 " model vdw 1.579 2.450 nonbonded pdb=" H SER D 92 " pdb=" OE2 GLU D 117 " model vdw 1.581 2.450 ... (remaining 175315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 5 through 133) selection = chain 'C' selection = (chain 'D' and resid 5 through 133) selection = (chain 'E' and resid 5 through 133) selection = (chain 'F' and resid 5 through 133) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.810 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6262 Z= 0.224 Angle : 0.586 5.641 8534 Z= 0.337 Chirality : 0.042 0.153 990 Planarity : 0.004 0.035 1078 Dihedral : 12.314 81.318 2238 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.43 % Favored : 98.44 % Rotamer: Outliers : 0.58 % Allowed : 5.67 % Favored : 93.75 % 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: -1.45 (0.30), residues: 768 helix: -1.15 (0.26), residues: 350 sheet: -0.32 (0.69), residues: 71 loop : -0.72 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 132 TYR 0.011 0.002 TYR A 102 PHE 0.009 0.001 PHE E 71 TRP 0.010 0.002 TRP A 10 HIS 0.005 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6262) covalent geometry : angle 0.58596 ( 8534) hydrogen bonds : bond 0.19914 ( 291) hydrogen bonds : angle 8.62538 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7618 (t-90) cc_final: 0.7381 (t-170) REVERT: A 34 VAL cc_start: 0.8592 (t) cc_final: 0.8373 (t) REVERT: B 100 VAL cc_start: 0.9080 (t) cc_final: 0.8855 (p) REVERT: B 132 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6815 (ptt90) REVERT: C 57 LYS cc_start: 0.8438 (mttt) cc_final: 0.8123 (mttm) REVERT: C 70 MET cc_start: 0.8604 (ttp) cc_final: 0.8342 (ttm) REVERT: C 107 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7530 (mt-10) REVERT: D 84 TYR cc_start: 0.7362 (m-80) cc_final: 0.7107 (m-80) REVERT: D 126 LYS cc_start: 0.8183 (tptt) cc_final: 0.7227 (tptp) REVERT: E 28 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7185 (tp30) REVERT: E 65 GLN cc_start: 0.8508 (tp40) cc_final: 0.8272 (tp40) REVERT: E 90 ASP cc_start: 0.7960 (m-30) cc_final: 0.7688 (t0) REVERT: E 107 GLU cc_start: 0.8071 (tt0) cc_final: 0.7742 (tt0) REVERT: E 115 LEU cc_start: 0.8799 (tp) cc_final: 0.8543 (tp) REVERT: F 16 TYR cc_start: 0.7709 (m-80) cc_final: 0.7281 (m-10) REVERT: F 111 SER cc_start: 0.7742 (m) cc_final: 0.7502 (t) outliers start: 4 outliers final: 3 residues processed: 228 average time/residue: 0.2304 time to fit residues: 65.0160 Evaluate side-chains 181 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 20 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 93 HIS A 101 GLN B 5 ASN B 65 GLN C 65 GLN D 13 HIS E 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.109611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089979 restraints weight = 36519.020| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.67 r_work: 0.3229 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6262 Z= 0.162 Angle : 0.582 5.716 8534 Z= 0.322 Chirality : 0.044 0.165 990 Planarity : 0.004 0.032 1078 Dihedral : 6.980 68.182 856 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.02 (0.30), residues: 768 helix: -0.61 (0.26), residues: 367 sheet: -0.14 (0.72), residues: 60 loop : -0.68 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 132 TYR 0.011 0.001 TYR E 102 PHE 0.015 0.001 PHE C 66 TRP 0.007 0.002 TRP A 10 HIS 0.006 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6262) covalent geometry : angle 0.58217 ( 8534) hydrogen bonds : bond 0.05032 ( 291) hydrogen bonds : angle 6.10905 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.8561 (t) cc_final: 0.8321 (t) REVERT: A 84 TYR cc_start: 0.8190 (m-10) cc_final: 0.7988 (m-10) REVERT: A 90 ASP cc_start: 0.8374 (m-30) cc_final: 0.8133 (m-30) REVERT: B 100 VAL cc_start: 0.9050 (t) cc_final: 0.8810 (p) REVERT: B 132 ARG cc_start: 0.7095 (ptt90) cc_final: 0.6848 (ptt90) REVERT: C 57 LYS cc_start: 0.8047 (mttt) cc_final: 0.7735 (mttm) REVERT: C 70 MET cc_start: 0.8626 (ttp) cc_final: 0.8415 (ttm) REVERT: D 117 GLU cc_start: 0.8013 (tt0) cc_final: 0.7674 (tt0) REVERT: D 126 LYS cc_start: 0.8101 (tptt) cc_final: 0.7200 (tptp) REVERT: E 65 GLN cc_start: 0.8420 (tp40) cc_final: 0.8060 (tp40) REVERT: E 90 ASP cc_start: 0.8075 (m-30) cc_final: 0.7688 (t0) REVERT: E 107 GLU cc_start: 0.8140 (tt0) cc_final: 0.7797 (tt0) REVERT: E 115 LEU cc_start: 0.8685 (tp) cc_final: 0.8341 (tp) REVERT: F 111 SER cc_start: 0.7572 (m) cc_final: 0.7263 (t) outliers start: 11 outliers final: 11 residues processed: 198 average time/residue: 0.2386 time to fit residues: 58.5968 Evaluate side-chains 187 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090161 restraints weight = 37080.212| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.64 r_work: 0.3227 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6262 Z= 0.151 Angle : 0.533 5.077 8534 Z= 0.291 Chirality : 0.043 0.157 990 Planarity : 0.004 0.028 1078 Dihedral : 6.833 69.152 856 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 11.05 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.30), residues: 768 helix: -0.31 (0.27), residues: 367 sheet: -0.48 (0.68), residues: 60 loop : -0.65 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 132 TYR 0.012 0.001 TYR D 6 PHE 0.009 0.001 PHE C 66 TRP 0.008 0.002 TRP A 10 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6262) covalent geometry : angle 0.53264 ( 8534) hydrogen bonds : bond 0.04260 ( 291) hydrogen bonds : angle 5.52691 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.8642 (t) cc_final: 0.8433 (t) REVERT: A 36 TYR cc_start: 0.7905 (m-80) cc_final: 0.6982 (m-80) REVERT: A 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.8119 (m-30) REVERT: B 65 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7371 (tp-100) REVERT: B 100 VAL cc_start: 0.9019 (t) cc_final: 0.8729 (p) REVERT: B 132 ARG cc_start: 0.7079 (ptt90) cc_final: 0.6849 (ptt90) REVERT: C 57 LYS cc_start: 0.8095 (mttt) cc_final: 0.7836 (mttm) REVERT: C 70 MET cc_start: 0.8614 (ttp) cc_final: 0.8411 (ttm) REVERT: C 107 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 90 ASP cc_start: 0.6850 (m-30) cc_final: 0.6633 (m-30) REVERT: D 117 GLU cc_start: 0.7962 (tt0) cc_final: 0.7651 (tt0) REVERT: E 65 GLN cc_start: 0.8359 (tp40) cc_final: 0.8017 (tp40) REVERT: E 90 ASP cc_start: 0.8133 (m-30) cc_final: 0.7702 (t0) REVERT: E 115 LEU cc_start: 0.8665 (tp) cc_final: 0.8315 (tp) REVERT: F 36 TYR cc_start: 0.8010 (m-80) cc_final: 0.7167 (m-80) REVERT: F 70 MET cc_start: 0.8070 (ttp) cc_final: 0.7795 (ttp) REVERT: F 111 SER cc_start: 0.7574 (m) cc_final: 0.7272 (t) outliers start: 15 outliers final: 15 residues processed: 197 average time/residue: 0.2357 time to fit residues: 57.8596 Evaluate side-chains 192 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089394 restraints weight = 36724.146| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.63 r_work: 0.3214 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6262 Z= 0.193 Angle : 0.546 4.635 8534 Z= 0.301 Chirality : 0.044 0.151 990 Planarity : 0.004 0.029 1078 Dihedral : 6.877 69.755 856 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 2.76 % Allowed : 12.94 % Favored : 84.30 % 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: -0.94 (0.30), residues: 768 helix: -0.29 (0.27), residues: 366 sheet: -0.68 (0.67), residues: 60 loop : -0.84 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.013 0.002 TYR D 6 PHE 0.012 0.001 PHE C 66 TRP 0.009 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6262) covalent geometry : angle 0.54631 ( 8534) hydrogen bonds : bond 0.04091 ( 291) hydrogen bonds : angle 5.42839 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.8613 (t) cc_final: 0.8354 (t) REVERT: A 90 ASP cc_start: 0.8434 (m-30) cc_final: 0.8188 (m-30) REVERT: A 120 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7394 (ttp-110) REVERT: B 132 ARG cc_start: 0.7034 (ptt90) cc_final: 0.6809 (ptt90) REVERT: C 28 GLU cc_start: 0.7504 (mp0) cc_final: 0.7181 (mp0) REVERT: C 57 LYS cc_start: 0.8131 (mttt) cc_final: 0.7877 (mttm) REVERT: D 104 TYR cc_start: 0.8563 (m-80) cc_final: 0.8180 (m-80) REVERT: D 117 GLU cc_start: 0.8017 (tt0) cc_final: 0.7661 (tt0) REVERT: E 39 TYR cc_start: 0.5204 (OUTLIER) cc_final: 0.4129 (t80) REVERT: E 65 GLN cc_start: 0.8330 (tp40) cc_final: 0.8033 (tp40) REVERT: E 90 ASP cc_start: 0.8146 (m-30) cc_final: 0.7701 (t0) REVERT: E 115 LEU cc_start: 0.8660 (tp) cc_final: 0.8318 (tp) REVERT: F 36 TYR cc_start: 0.8029 (m-80) cc_final: 0.7324 (m-80) REVERT: F 111 SER cc_start: 0.7633 (m) cc_final: 0.7331 (t) outliers start: 19 outliers final: 17 residues processed: 192 average time/residue: 0.2423 time to fit residues: 57.7336 Evaluate side-chains 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089423 restraints weight = 36778.182| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.67 r_work: 0.3210 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6262 Z= 0.175 Angle : 0.532 4.496 8534 Z= 0.292 Chirality : 0.043 0.151 990 Planarity : 0.004 0.028 1078 Dihedral : 6.780 69.701 856 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 3.20 % Allowed : 13.52 % Favored : 83.28 % 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: -0.97 (0.30), residues: 768 helix: -0.26 (0.27), residues: 367 sheet: -0.82 (0.67), residues: 60 loop : -0.90 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.012 0.001 TYR D 6 PHE 0.015 0.001 PHE E 58 TRP 0.008 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6262) covalent geometry : angle 0.53239 ( 8534) hydrogen bonds : bond 0.03848 ( 291) hydrogen bonds : angle 5.28635 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.8616 (t) cc_final: 0.8352 (t) REVERT: A 90 ASP cc_start: 0.8462 (m-30) cc_final: 0.8228 (m-30) REVERT: B 65 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7492 (tp-100) REVERT: B 132 ARG cc_start: 0.6976 (ptt90) cc_final: 0.6764 (ptt90) REVERT: C 28 GLU cc_start: 0.7567 (mp0) cc_final: 0.7234 (mp0) REVERT: C 57 LYS cc_start: 0.8137 (mttt) cc_final: 0.7900 (mttm) REVERT: C 107 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7719 (mt-10) REVERT: D 104 TYR cc_start: 0.8546 (m-80) cc_final: 0.8170 (m-80) REVERT: D 117 GLU cc_start: 0.8047 (tt0) cc_final: 0.7712 (tt0) REVERT: E 39 TYR cc_start: 0.5287 (OUTLIER) cc_final: 0.4215 (t80) REVERT: E 65 GLN cc_start: 0.8304 (tp40) cc_final: 0.8016 (tp40) REVERT: E 90 ASP cc_start: 0.8200 (m-30) cc_final: 0.7710 (t0) REVERT: E 115 LEU cc_start: 0.8660 (tp) cc_final: 0.8316 (tp) REVERT: F 36 TYR cc_start: 0.8032 (m-80) cc_final: 0.7412 (m-80) REVERT: F 111 SER cc_start: 0.7672 (m) cc_final: 0.7370 (t) outliers start: 22 outliers final: 19 residues processed: 193 average time/residue: 0.2340 time to fit residues: 56.2481 Evaluate side-chains 194 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090405 restraints weight = 36384.239| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.63 r_work: 0.3237 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6262 Z= 0.121 Angle : 0.501 4.460 8534 Z= 0.272 Chirality : 0.043 0.149 990 Planarity : 0.004 0.027 1078 Dihedral : 6.542 69.035 856 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer: Outliers : 2.62 % Allowed : 14.97 % Favored : 82.41 % 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: -0.69 (0.30), residues: 768 helix: 0.01 (0.27), residues: 368 sheet: -0.83 (0.68), residues: 58 loop : -0.78 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.029 0.001 TYR E 104 PHE 0.011 0.001 PHE D 58 TRP 0.008 0.001 TRP A 10 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6262) covalent geometry : angle 0.50114 ( 8534) hydrogen bonds : bond 0.03450 ( 291) hydrogen bonds : angle 5.04809 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7530 (t-90) cc_final: 0.7194 (t-170) REVERT: A 36 TYR cc_start: 0.7845 (m-80) cc_final: 0.6856 (m-80) REVERT: A 84 TYR cc_start: 0.8114 (m-10) cc_final: 0.7732 (m-10) REVERT: A 90 ASP cc_start: 0.8415 (m-30) cc_final: 0.8155 (m-30) REVERT: B 65 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7502 (tp-100) REVERT: B 132 ARG cc_start: 0.6984 (ptt90) cc_final: 0.6665 (ptt90) REVERT: C 28 GLU cc_start: 0.7654 (mp0) cc_final: 0.7277 (mp0) REVERT: C 57 LYS cc_start: 0.8165 (mttt) cc_final: 0.7941 (mttm) REVERT: C 107 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 104 TYR cc_start: 0.8539 (m-80) cc_final: 0.8113 (m-80) REVERT: D 117 GLU cc_start: 0.8005 (tt0) cc_final: 0.7688 (tt0) REVERT: E 39 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4179 (t80) REVERT: E 65 GLN cc_start: 0.8309 (tp40) cc_final: 0.7996 (tp40) REVERT: E 90 ASP cc_start: 0.8176 (m-30) cc_final: 0.7684 (t0) REVERT: E 115 LEU cc_start: 0.8635 (tp) cc_final: 0.8297 (tp) REVERT: F 70 MET cc_start: 0.7996 (ttp) cc_final: 0.7693 (ttp) REVERT: F 111 SER cc_start: 0.7656 (m) cc_final: 0.7370 (t) outliers start: 18 outliers final: 14 residues processed: 192 average time/residue: 0.2384 time to fit residues: 56.9591 Evaluate side-chains 192 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089424 restraints weight = 36359.343| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.61 r_work: 0.3219 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6262 Z= 0.185 Angle : 0.530 4.458 8534 Z= 0.292 Chirality : 0.043 0.148 990 Planarity : 0.004 0.039 1078 Dihedral : 6.619 69.035 856 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 2.76 % Allowed : 15.55 % Favored : 81.69 % 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: -0.83 (0.30), residues: 768 helix: -0.06 (0.27), residues: 367 sheet: -0.89 (0.69), residues: 58 loop : -0.92 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.014 0.002 TYR E 104 PHE 0.017 0.001 PHE E 58 TRP 0.008 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6262) covalent geometry : angle 0.53037 ( 8534) hydrogen bonds : bond 0.03726 ( 291) hydrogen bonds : angle 5.14012 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TYR cc_start: 0.8004 (m-80) cc_final: 0.7454 (m-80) REVERT: A 90 ASP cc_start: 0.8430 (m-30) cc_final: 0.8193 (m-30) REVERT: B 65 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7514 (tp-100) REVERT: B 132 ARG cc_start: 0.7000 (ptt90) cc_final: 0.6685 (ptt90) REVERT: C 107 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 117 GLU cc_start: 0.8021 (tt0) cc_final: 0.7704 (tt0) REVERT: E 39 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.4268 (t80) REVERT: E 65 GLN cc_start: 0.8315 (tp40) cc_final: 0.8047 (tp40) REVERT: E 90 ASP cc_start: 0.8203 (m-30) cc_final: 0.7713 (t0) REVERT: F 111 SER cc_start: 0.7821 (m) cc_final: 0.7553 (t) outliers start: 19 outliers final: 17 residues processed: 189 average time/residue: 0.2339 time to fit residues: 55.4979 Evaluate side-chains 191 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 69 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090342 restraints weight = 36042.708| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.61 r_work: 0.3231 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6262 Z= 0.125 Angle : 0.497 4.438 8534 Z= 0.270 Chirality : 0.043 0.148 990 Planarity : 0.004 0.033 1078 Dihedral : 6.416 68.790 856 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer: Outliers : 2.47 % Allowed : 15.55 % Favored : 81.98 % 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: -0.58 (0.30), residues: 768 helix: 0.17 (0.28), residues: 367 sheet: -0.89 (0.70), residues: 58 loop : -0.78 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.015 0.001 TYR E 104 PHE 0.014 0.001 PHE E 58 TRP 0.007 0.001 TRP F 10 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6262) covalent geometry : angle 0.49708 ( 8534) hydrogen bonds : bond 0.03356 ( 291) hydrogen bonds : angle 4.96119 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7556 (t-90) cc_final: 0.7212 (t-170) REVERT: A 36 TYR cc_start: 0.8009 (m-80) cc_final: 0.7475 (m-80) REVERT: A 84 TYR cc_start: 0.8095 (m-10) cc_final: 0.7816 (m-10) REVERT: A 90 ASP cc_start: 0.8425 (m-30) cc_final: 0.8176 (m-30) REVERT: B 65 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7507 (tp-100) REVERT: B 132 ARG cc_start: 0.6968 (ptt90) cc_final: 0.6650 (ptt90) REVERT: C 28 GLU cc_start: 0.7759 (mp0) cc_final: 0.7288 (mp0) REVERT: C 107 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7737 (mt-10) REVERT: D 117 GLU cc_start: 0.8034 (tt0) cc_final: 0.7737 (tt0) REVERT: E 39 TYR cc_start: 0.5262 (OUTLIER) cc_final: 0.4215 (t80) REVERT: E 65 GLN cc_start: 0.8309 (tp40) cc_final: 0.8020 (tp40) REVERT: E 90 ASP cc_start: 0.8191 (m-30) cc_final: 0.7706 (t0) REVERT: F 111 SER cc_start: 0.7805 (m) cc_final: 0.7545 (t) outliers start: 17 outliers final: 15 residues processed: 190 average time/residue: 0.2221 time to fit residues: 52.8510 Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090390 restraints weight = 36422.743| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.65 r_work: 0.3235 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6262 Z= 0.122 Angle : 0.494 4.506 8534 Z= 0.267 Chirality : 0.043 0.147 990 Planarity : 0.004 0.031 1078 Dihedral : 6.263 69.037 856 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 2.33 % Allowed : 15.41 % Favored : 82.27 % 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: -0.45 (0.31), residues: 768 helix: 0.29 (0.28), residues: 368 sheet: -0.86 (0.70), residues: 58 loop : -0.74 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.016 0.001 TYR A 25 PHE 0.013 0.001 PHE E 58 TRP 0.009 0.001 TRP F 10 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6262) covalent geometry : angle 0.49363 ( 8534) hydrogen bonds : bond 0.03214 ( 291) hydrogen bonds : angle 4.88237 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7539 (t-90) cc_final: 0.7201 (t-170) REVERT: A 36 TYR cc_start: 0.7974 (m-80) cc_final: 0.7522 (m-80) REVERT: A 39 TYR cc_start: 0.7785 (t80) cc_final: 0.7415 (t80) REVERT: A 90 ASP cc_start: 0.8439 (m-30) cc_final: 0.8169 (m-30) REVERT: B 65 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7514 (tp-100) REVERT: B 132 ARG cc_start: 0.6950 (ptt90) cc_final: 0.6641 (ptt90) REVERT: C 28 GLU cc_start: 0.7767 (mp0) cc_final: 0.7269 (mp0) REVERT: C 107 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 117 GLU cc_start: 0.8061 (tt0) cc_final: 0.7772 (tt0) REVERT: E 39 TYR cc_start: 0.5273 (OUTLIER) cc_final: 0.4274 (t80) REVERT: E 90 ASP cc_start: 0.8204 (m-30) cc_final: 0.7713 (t0) REVERT: F 111 SER cc_start: 0.7806 (m) cc_final: 0.7538 (t) outliers start: 16 outliers final: 15 residues processed: 189 average time/residue: 0.2209 time to fit residues: 52.4925 Evaluate side-chains 190 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090622 restraints weight = 36412.344| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.62 r_work: 0.3233 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6262 Z= 0.129 Angle : 0.494 4.460 8534 Z= 0.268 Chirality : 0.043 0.152 990 Planarity : 0.004 0.030 1078 Dihedral : 6.215 68.671 856 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.31), residues: 768 helix: 0.33 (0.28), residues: 368 sheet: -0.93 (0.70), residues: 58 loop : -0.74 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.016 0.001 TYR A 25 PHE 0.013 0.001 PHE E 58 TRP 0.009 0.001 TRP F 10 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6262) covalent geometry : angle 0.49445 ( 8534) hydrogen bonds : bond 0.03238 ( 291) hydrogen bonds : angle 4.85929 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 HIS cc_start: 0.7563 (t-90) cc_final: 0.7220 (t-170) REVERT: A 36 TYR cc_start: 0.7998 (m-80) cc_final: 0.7556 (m-80) REVERT: A 39 TYR cc_start: 0.7762 (t80) cc_final: 0.7390 (t80) REVERT: A 90 ASP cc_start: 0.8464 (m-30) cc_final: 0.8205 (m-30) REVERT: B 65 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7516 (tp-100) REVERT: C 107 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 104 TYR cc_start: 0.8571 (m-80) cc_final: 0.8107 (m-80) REVERT: D 117 GLU cc_start: 0.8060 (tt0) cc_final: 0.7768 (tt0) REVERT: E 39 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4310 (t80) REVERT: E 65 GLN cc_start: 0.8324 (tp40) cc_final: 0.8019 (tp40) REVERT: E 90 ASP cc_start: 0.8214 (m-30) cc_final: 0.7704 (t0) REVERT: F 111 SER cc_start: 0.7818 (m) cc_final: 0.7542 (t) outliers start: 17 outliers final: 16 residues processed: 187 average time/residue: 0.2268 time to fit residues: 53.3467 Evaluate side-chains 191 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089933 restraints weight = 36432.599| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.63 r_work: 0.3224 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6262 Z= 0.162 Angle : 0.513 4.535 8534 Z= 0.279 Chirality : 0.043 0.149 990 Planarity : 0.004 0.030 1078 Dihedral : 6.267 68.939 856 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 2.76 % Allowed : 15.55 % Favored : 81.69 % 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: -0.52 (0.31), residues: 768 helix: 0.27 (0.28), residues: 368 sheet: -0.99 (0.70), residues: 58 loop : -0.81 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 132 TYR 0.016 0.002 TYR A 25 PHE 0.010 0.001 PHE D 58 TRP 0.008 0.002 TRP F 10 HIS 0.004 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6262) covalent geometry : angle 0.51309 ( 8534) hydrogen bonds : bond 0.03379 ( 291) hydrogen bonds : angle 4.95580 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.78 seconds wall clock time: 57 minutes 57.73 seconds (3477.73 seconds total)