Starting phenix.real_space_refine on Wed Jul 30 07:07:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc6_19049/07_2025/8rc6_19049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc6_19049/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc6_19049/07_2025/8rc6_19049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc6_19049/07_2025/8rc6_19049.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc6_19049/07_2025/8rc6_19049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc6_19049/07_2025/8rc6_19049.cif" } resolution = 3.3 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.09, per 1000 atoms: 0.66 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: 3.42 Conformation dependent library (CDL) restraints added in 987.0 milliseconds 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: 1.03 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: 4.19 Time building geometry restraints manager: 4.10 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: 0.01 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: 16.700 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: 0.220 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.350 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.30), residues: 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 TRP 0.010 0.002 TRP A 10 HIS 0.005 0.001 HIS D 13 PHE 0.009 0.001 PHE E 71 TYR 0.011 0.002 TYR A 102 ARG 0.003 0.001 ARG E 132 Details of bonding type rmsd hydrogen bonds : bond 0.19914 ( 291) hydrogen bonds : angle 8.62538 ( 819) covalent geometry : bond 0.00469 ( 6262) covalent geometry : angle 0.58596 ( 8534) *********************** 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 : 0.953 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: 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 90 ASP cc_start: 0.7343 (t70) cc_final: 0.7111 (t0) 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: 0.7103 (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: 0.7184 (tp30) REVERT: E 65 GLN cc_start: 0.8508 (tp40) cc_final: 0.8271 (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: 0.7503 (t) outliers start: 4 outliers final: 3 residues processed: 228 average time/residue: 0.4798 time to fit residues: 135.6604 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 : 0.946 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089812 restraints weight = 36555.530| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.65 r_work: 0.3225 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1912 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= 0.169 Angle : 0.578 5.368 8534 Z= 0.320 Chirality : 0.044 0.161 990 Planarity : 0.004 0.044 1078 Dihedral : 7.012 68.562 856 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 1.60 % Allowed : 11.77 % Favored : 86.63 % 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: -1.10 (0.30), residues: 768 helix: -0.66 (0.26), residues: 368 sheet: -0.16 (0.71), residues: 60 loop : -0.74 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 10 HIS 0.006 0.001 HIS B 13 PHE 0.014 0.001 PHE C 66 TYR 0.011 0.001 TYR E 102 ARG 0.004 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 291) hydrogen bonds : angle 6.10613 ( 819) covalent geometry : bond 0.00360 ( 6262) covalent geometry : angle 0.57801 ( 8534) *********************** 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 200 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.927 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: 0.8576 (t) cc_final: 0.8340 (t) REVERT: A 90 ASP cc_start: 0.8345 (m-30) cc_final: 0.8115 (m-30) REVERT: B 100 VAL cc_start: 0.9050 (t) cc_final: 0.8814 (p) REVERT: B 132 ARG cc_start: 0.7082 (ptt90) cc_final: 0.6841 (ptt90) REVERT: C 57 LYS cc_start: 0.8093 (mttt) cc_final: 0.7781 (mttm) REVERT: C 70 MET cc_start: 0.8612 (ttp) cc_final: 0.8394 (ttm) REVERT: D 90 ASP cc_start: 0.6848 (m-30) cc_final: 0.6586 (m-30) REVERT: D 117 GLU cc_start: 0.7992 (tt0) cc_final: 0.7649 (tt0) REVERT: D 126 LYS cc_start: 0.8098 (tptt) cc_final: 0.7201 (tptp) REVERT: E 65 GLN cc_start: 0.8397 (tp40) cc_final: 0.8048 (tp40) REVERT: E 90 ASP cc_start: 0.8062 (m-30) cc_final: 0.7698 (t0) REVERT: E 107 GLU cc_start: 0.8114 (tt0) cc_final: 0.7769 (tt0) REVERT: E 115 LEU cc_start: 0.8714 (tp) cc_final: 0.8367 (tp) REVERT: F 36 TYR cc_start: 0.7954 (m-80) cc_final: 0.7042 (m-80) REVERT: F 111 SER cc_start: 0.7603 (m) cc_final: 0.7302 (t) outliers start: 11 outliers final: 11 residues processed: 196 average time/residue: 0.4703 time to fit residues: 115.8911 Evaluate side-chains 188 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.110022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090597 restraints weight = 36793.476| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.65 r_work: 0.3236 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6262 Z= 0.133 Angle : 0.523 5.063 8534 Z= 0.284 Chirality : 0.043 0.160 990 Planarity : 0.004 0.028 1078 Dihedral : 6.739 68.984 856 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.40 % Rotamer: Outliers : 2.03 % Allowed : 11.34 % Favored : 86.63 % 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: -0.75 (0.30), residues: 768 helix: -0.27 (0.27), residues: 367 sheet: -0.43 (0.68), residues: 60 loop : -0.60 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.004 0.001 HIS A 13 PHE 0.008 0.001 PHE D 58 TYR 0.013 0.001 TYR C 6 ARG 0.001 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 291) hydrogen bonds : angle 5.46150 ( 819) covalent geometry : bond 0.00289 ( 6262) covalent geometry : angle 0.52310 ( 8534) *********************** 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 204 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 1.047 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 7 HIS cc_start: 0.7510 (t-90) cc_final: 0.7248 (t-170) REVERT: A 34 VAL cc_start: 0.8660 (t) cc_final: 0.8428 (t) REVERT: A 36 TYR cc_start: 0.7946 (m-80) cc_final: 0.6971 (m-80) REVERT: A 84 TYR cc_start: 0.8138 (m-10) cc_final: 0.7882 (m-10) REVERT: A 90 ASP cc_start: 0.8393 (m-30) cc_final: 0.8124 (m-30) REVERT: B 65 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7356 (tp-100) REVERT: B 100 VAL cc_start: 0.9009 (t) cc_final: 0.8717 (p) REVERT: B 132 ARG cc_start: 0.7069 (ptt90) cc_final: 0.6831 (ptt90) REVERT: C 107 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 90 ASP cc_start: 0.6874 (m-30) cc_final: 0.6661 (m-30) REVERT: D 117 GLU cc_start: 0.7982 (tt0) cc_final: 0.7677 (tt0) REVERT: E 65 GLN cc_start: 0.8327 (tp40) cc_final: 0.7987 (tp40) REVERT: E 90 ASP cc_start: 0.8111 (m-30) cc_final: 0.7681 (t0) REVERT: E 115 LEU cc_start: 0.8659 (tp) cc_final: 0.8305 (tp) REVERT: F 36 TYR cc_start: 0.7992 (m-80) cc_final: 0.7157 (m-80) REVERT: F 111 SER cc_start: 0.7584 (m) cc_final: 0.7282 (t) outliers start: 14 outliers final: 13 residues processed: 199 average time/residue: 0.5182 time to fit residues: 129.0363 Evaluate side-chains 192 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 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 = 0.3671 r_free = 0.3671 target = 0.109053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089469 restraints weight = 36190.506| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.65 r_work: 0.3216 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6262 Z= 0.192 Angle : 0.545 4.594 8534 Z= 0.300 Chirality : 0.044 0.152 990 Planarity : 0.004 0.028 1078 Dihedral : 6.837 69.824 856 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 2.33 % Allowed : 13.23 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.30), residues: 768 helix: -0.24 (0.27), residues: 366 sheet: -0.69 (0.66), residues: 60 loop : -0.81 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 PHE 0.013 0.001 PHE C 66 TYR 0.014 0.002 TYR D 6 ARG 0.003 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 291) hydrogen bonds : angle 5.38523 ( 819) covalent geometry : bond 0.00415 ( 6262) covalent geometry : angle 0.54523 ( 8534) *********************** 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 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.375 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 7 HIS cc_start: 0.7560 (t-90) cc_final: 0.7289 (t-170) REVERT: A 34 VAL cc_start: 0.8623 (t) cc_final: 0.8404 (t) REVERT: A 36 TYR cc_start: 0.8010 (m-80) cc_final: 0.7047 (m-80) REVERT: A 90 ASP cc_start: 0.8413 (m-30) cc_final: 0.8177 (m-30) REVERT: A 120 ARG cc_start: 0.7720 (ttp-110) cc_final: 0.7381 (ttp-110) REVERT: B 65 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7452 (tp-100) REVERT: B 132 ARG cc_start: 0.7040 (ptt90) cc_final: 0.6817 (ptt90) REVERT: D 104 TYR cc_start: 0.8571 (m-80) cc_final: 0.8182 (m-80) REVERT: D 117 GLU cc_start: 0.7995 (tt0) cc_final: 0.7630 (tt0) REVERT: E 39 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.4104 (t80) REVERT: E 65 GLN cc_start: 0.8326 (tp40) cc_final: 0.8039 (tp40) REVERT: E 90 ASP cc_start: 0.8118 (m-30) cc_final: 0.7695 (t0) REVERT: E 115 LEU cc_start: 0.8661 (tp) cc_final: 0.8316 (tp) REVERT: F 36 TYR cc_start: 0.8042 (m-80) cc_final: 0.7331 (m-80) REVERT: F 111 SER cc_start: 0.7634 (m) cc_final: 0.7332 (t) outliers start: 16 outliers final: 15 residues processed: 190 average time/residue: 0.5562 time to fit residues: 133.8261 Evaluate side-chains 194 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain E residue 39 TYR 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 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 55 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089992 restraints weight = 36417.457| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.66 r_work: 0.3228 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6262 Z= 0.141 Angle : 0.512 4.647 8534 Z= 0.279 Chirality : 0.043 0.162 990 Planarity : 0.004 0.028 1078 Dihedral : 6.648 69.437 856 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.47 % Allowed : 13.95 % Favored : 83.58 % 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: -0.75 (0.30), residues: 768 helix: -0.12 (0.27), residues: 368 sheet: -0.74 (0.66), residues: 60 loop : -0.74 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.004 0.001 HIS A 13 PHE 0.016 0.001 PHE E 58 TYR 0.012 0.001 TYR D 6 ARG 0.002 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 291) hydrogen bonds : angle 5.17503 ( 819) covalent geometry : bond 0.00306 ( 6262) covalent geometry : angle 0.51219 ( 8534) *********************** 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 196 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 1.130 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: 0.7521 (t-90) cc_final: 0.7244 (t-170) REVERT: A 34 VAL cc_start: 0.8624 (t) cc_final: 0.8413 (t) REVERT: A 36 TYR cc_start: 0.7960 (m-80) cc_final: 0.6972 (m-80) REVERT: A 90 ASP cc_start: 0.8432 (m-30) cc_final: 0.8189 (m-30) REVERT: B 65 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7488 (tp-100) REVERT: B 132 ARG cc_start: 0.6967 (ptt90) cc_final: 0.6758 (ptt90) REVERT: C 28 GLU cc_start: 0.7615 (mp0) cc_final: 0.7231 (mp0) REVERT: C 107 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7711 (mt-10) REVERT: D 104 TYR cc_start: 0.8543 (m-80) cc_final: 0.8152 (m-80) REVERT: D 117 GLU cc_start: 0.8023 (tt0) cc_final: 0.7676 (tt0) REVERT: E 39 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.4158 (t80) REVERT: E 65 GLN cc_start: 0.8310 (tp40) cc_final: 0.7995 (tp40) REVERT: E 90 ASP cc_start: 0.8139 (m-30) cc_final: 0.7680 (t0) REVERT: E 115 LEU cc_start: 0.8637 (tp) cc_final: 0.8295 (tp) REVERT: F 36 TYR cc_start: 0.8003 (m-80) cc_final: 0.7333 (m-80) REVERT: F 111 SER cc_start: 0.7612 (m) cc_final: 0.7308 (t) outliers start: 17 outliers final: 14 residues processed: 189 average time/residue: 0.5418 time to fit residues: 130.8916 Evaluate side-chains 189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090258 restraints weight = 36838.746| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.64 r_work: 0.3235 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2891 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= 0.138 Angle : 0.506 4.442 8534 Z= 0.275 Chirality : 0.043 0.151 990 Planarity : 0.004 0.027 1078 Dihedral : 6.530 68.970 856 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.65 % Favored : 96.22 % Rotamer: Outliers : 2.62 % Allowed : 14.68 % Favored : 82.70 % 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: -0.67 (0.30), residues: 768 helix: 0.00 (0.27), residues: 367 sheet: -0.85 (0.67), residues: 58 loop : -0.74 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.004 0.001 HIS A 13 PHE 0.017 0.001 PHE E 58 TYR 0.030 0.001 TYR E 104 ARG 0.002 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 291) hydrogen bonds : angle 5.07081 ( 819) covalent geometry : bond 0.00299 ( 6262) covalent geometry : angle 0.50604 ( 8534) *********************** 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 201 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.963 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 7 HIS cc_start: 0.7521 (t-90) cc_final: 0.7252 (t-170) REVERT: A 36 TYR cc_start: 0.7880 (m-80) cc_final: 0.6945 (m-80) REVERT: A 84 TYR cc_start: 0.8129 (m-10) cc_final: 0.7919 (m-10) REVERT: A 90 ASP cc_start: 0.8426 (m-30) cc_final: 0.8165 (m-30) REVERT: A 119 LEU cc_start: 0.8780 (mt) cc_final: 0.8544 (mt) REVERT: B 65 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7507 (tp-100) REVERT: B 132 ARG cc_start: 0.7006 (ptt90) cc_final: 0.6690 (ptt90) REVERT: C 107 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 18 ASN cc_start: 0.8586 (t0) cc_final: 0.8239 (t0) REVERT: D 104 TYR cc_start: 0.8541 (m-80) cc_final: 0.8101 (m-80) REVERT: D 117 GLU cc_start: 0.8013 (tt0) cc_final: 0.7682 (tt0) REVERT: E 39 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4188 (t80) REVERT: E 65 GLN cc_start: 0.8305 (tp40) cc_final: 0.8009 (tp40) REVERT: E 90 ASP cc_start: 0.8175 (m-30) cc_final: 0.7699 (t0) REVERT: E 115 LEU cc_start: 0.8622 (tp) cc_final: 0.8287 (tp) REVERT: F 111 SER cc_start: 0.7633 (m) cc_final: 0.7336 (t) outliers start: 18 outliers final: 16 residues processed: 192 average time/residue: 0.4688 time to fit residues: 112.4206 Evaluate side-chains 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 77 THR 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 76 ILE 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 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3666 r_free = 0.3666 target = 0.108489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089100 restraints weight = 36741.896| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.62 r_work: 0.3214 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6262 Z= 0.198 Angle : 0.549 4.471 8534 Z= 0.300 Chirality : 0.044 0.169 990 Planarity : 0.004 0.029 1078 Dihedral : 6.615 69.201 856 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 2.91 % Allowed : 14.97 % 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 (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: -0.92 (0.30), residues: 768 helix: -0.14 (0.27), residues: 367 sheet: -0.96 (0.68), residues: 58 loop : -0.95 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 PHE 0.016 0.002 PHE E 58 TYR 0.014 0.002 TYR D 6 ARG 0.003 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 291) hydrogen bonds : angle 5.17774 ( 819) covalent geometry : bond 0.00428 ( 6262) covalent geometry : angle 0.54937 ( 8534) *********************** 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: 20 poor density : 176 time to evaluate : 1.135 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 7 HIS cc_start: 0.7581 (t-90) cc_final: 0.7317 (t-170) REVERT: A 36 TYR cc_start: 0.8113 (m-80) cc_final: 0.7675 (m-80) REVERT: A 90 ASP cc_start: 0.8436 (m-30) cc_final: 0.8204 (m-30) REVERT: B 65 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7530 (tp-100) REVERT: C 28 GLU cc_start: 0.7762 (mp0) cc_final: 0.7294 (mp0) REVERT: C 107 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7727 (mt-10) REVERT: D 18 ASN cc_start: 0.8587 (t0) cc_final: 0.8227 (t0) REVERT: D 117 GLU cc_start: 0.8003 (tt0) cc_final: 0.7678 (tt0) REVERT: E 39 TYR cc_start: 0.5383 (OUTLIER) cc_final: 0.4304 (t80) REVERT: E 65 GLN cc_start: 0.8317 (tp40) cc_final: 0.8048 (tp40) REVERT: E 90 ASP cc_start: 0.8191 (m-30) cc_final: 0.7703 (t0) REVERT: F 111 SER cc_start: 0.7802 (m) cc_final: 0.7529 (t) outliers start: 20 outliers final: 18 residues processed: 188 average time/residue: 0.5200 time to fit residues: 125.4017 Evaluate side-chains 191 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 80 ASN 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 76 ILE 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 51 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 69 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: ** 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 = 0.3654 r_free = 0.3654 target = 0.108050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088052 restraints weight = 37190.048| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.83 r_work: 0.3181 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6262 Z= 0.198 Angle : 0.549 4.541 8534 Z= 0.300 Chirality : 0.044 0.180 990 Planarity : 0.004 0.037 1078 Dihedral : 6.624 69.070 856 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.63 % Allowed : 14.83 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.30), residues: 768 helix: -0.13 (0.27), residues: 366 sheet: -1.04 (0.70), residues: 58 loop : -1.05 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 10 HIS 0.005 0.001 HIS E 13 PHE 0.014 0.001 PHE E 58 TYR 0.015 0.002 TYR E 104 ARG 0.004 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 291) hydrogen bonds : angle 5.19326 ( 819) covalent geometry : bond 0.00430 ( 6262) covalent geometry : angle 0.54933 ( 8534) *********************** 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 201 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.982 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 36 TYR cc_start: 0.8157 (m-80) cc_final: 0.7752 (m-80) REVERT: A 84 TYR cc_start: 0.8132 (m-10) cc_final: 0.7871 (m-10) REVERT: B 65 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7516 (tp-100) REVERT: C 28 GLU cc_start: 0.7768 (mp0) cc_final: 0.7310 (mp0) REVERT: C 107 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 13 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7479 (t-90) REVERT: D 18 ASN cc_start: 0.8579 (t0) cc_final: 0.8195 (t0) REVERT: D 117 GLU cc_start: 0.8016 (tt0) cc_final: 0.7718 (tt0) REVERT: E 39 TYR cc_start: 0.5516 (OUTLIER) cc_final: 0.4413 (t80) REVERT: E 65 GLN cc_start: 0.8318 (tp40) cc_final: 0.8064 (tp40) REVERT: E 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7738 (t0) REVERT: F 111 SER cc_start: 0.7984 (m) cc_final: 0.7721 (t) outliers start: 25 outliers final: 21 residues processed: 192 average time/residue: 0.4772 time to fit residues: 115.7704 Evaluate side-chains 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 13 HIS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 80 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.108703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089408 restraints weight = 36692.791| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.62 r_work: 0.3215 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3114 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= 0.173 Angle : 0.535 4.532 8534 Z= 0.291 Chirality : 0.043 0.152 990 Planarity : 0.004 0.037 1078 Dihedral : 6.541 68.681 856 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.92 % Rotamer: Outliers : 3.05 % Allowed : 15.84 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.30), residues: 768 helix: -0.07 (0.27), residues: 367 sheet: -0.98 (0.71), residues: 58 loop : -1.09 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 10 HIS 0.004 0.001 HIS E 13 PHE 0.013 0.001 PHE E 58 TYR 0.014 0.002 TYR A 25 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 291) hydrogen bonds : angle 5.12155 ( 819) covalent geometry : bond 0.00379 ( 6262) covalent geometry : angle 0.53471 ( 8534) *********************** 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 199 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.948 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: A 7 HIS cc_start: 0.7597 (t-90) cc_final: 0.7331 (t-170) REVERT: A 36 TYR cc_start: 0.8076 (m-80) cc_final: 0.7832 (m-80) REVERT: B 65 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7502 (tp-100) REVERT: C 28 GLU cc_start: 0.7769 (mp0) cc_final: 0.7293 (mp0) REVERT: C 107 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 13 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7466 (t-90) REVERT: D 18 ASN cc_start: 0.8575 (t0) cc_final: 0.8191 (t0) REVERT: D 117 GLU cc_start: 0.8042 (tt0) cc_final: 0.7743 (tt0) REVERT: E 39 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.4362 (t80) REVERT: E 65 GLN cc_start: 0.8291 (tp40) cc_final: 0.8022 (tp40) REVERT: E 90 ASP cc_start: 0.8206 (m-30) cc_final: 0.7715 (t0) REVERT: F 111 SER cc_start: 0.8026 (m) cc_final: 0.7750 (t) outliers start: 21 outliers final: 19 residues processed: 190 average time/residue: 0.5852 time to fit residues: 140.4009 Evaluate side-chains 198 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 13 HIS 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 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 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 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.109318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089986 restraints weight = 36298.010| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.63 r_work: 0.3224 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3255 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= 0.132 Angle : 0.514 4.499 8534 Z= 0.277 Chirality : 0.043 0.164 990 Planarity : 0.004 0.033 1078 Dihedral : 6.341 68.670 856 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 2.47 % Allowed : 16.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.30), residues: 768 helix: 0.11 (0.27), residues: 368 sheet: -0.99 (0.70), residues: 58 loop : -0.94 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 10 HIS 0.004 0.001 HIS A 13 PHE 0.012 0.001 PHE D 58 TYR 0.015 0.002 TYR A 25 ARG 0.004 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 291) hydrogen bonds : angle 4.97845 ( 819) covalent geometry : bond 0.00291 ( 6262) covalent geometry : angle 0.51405 ( 8534) ********************** 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 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.040 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: A 7 HIS cc_start: 0.7554 (t-90) cc_final: 0.7287 (t-170) REVERT: A 36 TYR cc_start: 0.8023 (m-80) cc_final: 0.7678 (m-80) REVERT: A 39 TYR cc_start: 0.7773 (t80) cc_final: 0.7394 (t80) REVERT: A 84 TYR cc_start: 0.8108 (m-10) cc_final: 0.7890 (m-10) REVERT: B 65 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7522 (tp-100) REVERT: C 28 GLU cc_start: 0.7796 (mp0) cc_final: 0.7273 (mp0) REVERT: D 18 ASN cc_start: 0.8564 (t0) cc_final: 0.8204 (t0) REVERT: D 117 GLU cc_start: 0.8045 (tt0) cc_final: 0.7755 (tt0) REVERT: E 39 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.4352 (t80) REVERT: E 65 GLN cc_start: 0.8300 (tp40) cc_final: 0.8012 (tp40) REVERT: E 90 ASP cc_start: 0.8202 (m-30) cc_final: 0.7706 (t0) REVERT: F 111 SER cc_start: 0.8026 (m) cc_final: 0.7743 (t) outliers start: 17 outliers final: 15 residues processed: 188 average time/residue: 0.4709 time to fit residues: 111.3576 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 : 1.006 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 0.0070 chunk 45 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 overall best weight: 0.1576 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.110400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091176 restraints weight = 36278.487| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.63 r_work: 0.3249 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6262 Z= 0.098 Angle : 0.496 5.139 8534 Z= 0.264 Chirality : 0.043 0.161 990 Planarity : 0.004 0.031 1078 Dihedral : 6.021 68.933 856 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer: Outliers : 2.18 % Allowed : 16.72 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 768 helix: 0.42 (0.28), residues: 368 sheet: -1.04 (0.68), residues: 58 loop : -0.76 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 10 HIS 0.005 0.001 HIS A 13 PHE 0.014 0.001 PHE D 58 TYR 0.017 0.001 TYR A 25 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 291) hydrogen bonds : angle 4.75595 ( 819) covalent geometry : bond 0.00223 ( 6262) covalent geometry : angle 0.49634 ( 8534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6987.04 seconds wall clock time: 124 minutes 13.16 seconds (7453.16 seconds total)