Starting phenix.real_space_refine on Sun Nov 17 02:09:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/11_2024/8pc5_17594.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 13 5.16 5 C 7172 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 8.70, per 1000 atoms: 0.68 Number of scatterers: 12836 At special positions: 0 Unit cell: (102.533, 125.04, 123.373, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 64.4% alpha, 5.0% beta 146 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.595A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.605A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.817A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.702A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.528A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.523A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.783A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.399A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.113A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.607A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.345A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.577A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.363A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.850A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2069 1.33 - 1.45: 4662 1.45 - 1.57: 6333 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13676 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.758 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" P DT J -72 " pdb=" OP1 DT J -72 " ideal model delta sigma weight residual 1.480 1.522 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" P DC I 69 " pdb=" OP2 DC I 69 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" P DG J 62 " pdb=" OP1 DG J 62 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 ... (remaining 13671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18671 1.67 - 3.33: 963 3.33 - 5.00: 68 5.00 - 6.66: 17 6.66 - 8.33: 11 Bond angle restraints: 19730 Sorted by residual: angle pdb=" O3' DC I 49 " pdb=" P DA I 50 " pdb=" O5' DA I 50 " ideal model delta sigma weight residual 104.00 95.83 8.17 1.50e+00 4.44e-01 2.97e+01 angle pdb=" C4' DC I 49 " pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 110.00 102.83 7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" O3' DA J -73 " pdb=" P DT J -72 " pdb=" O5' DT J -72 " ideal model delta sigma weight residual 104.00 109.54 -5.54 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sigma weight residual 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sigma weight residual 120.20 125.25 -5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 5857 35.94 - 71.87: 1586 71.87 - 107.81: 28 107.81 - 143.75: 3 143.75 - 179.69: 3 Dihedral angle restraints: 7477 sinusoidal: 5003 harmonic: 2474 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual -140.00 39.69 -179.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.29 -165.29 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.69 -158.69 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2146 0.113 - 0.226: 73 0.226 - 0.340: 0 0.340 - 0.453: 1 0.453 - 0.566: 9 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 65 " pdb=" OP1 DA J 65 " pdb=" OP2 DA J 65 " pdb=" O5' DA J 65 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" P DG J 64 " pdb=" OP1 DG J 64 " pdb=" OP2 DG J 64 " pdb=" O5' DG J 64 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 2226 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ML3 A 36 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ML3 A 36 " -0.049 2.00e-02 2.50e+03 pdb=" O ML3 A 36 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 37 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " -0.029 2.00e-02 2.50e+03 1.85e-02 7.74e+00 pdb=" N1 DC I 49 " 0.043 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.032 2.00e-02 2.50e+03 1.56e-02 7.29e+00 pdb=" N9 DG I 47 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1385 2.74 - 3.28: 10741 3.28 - 3.82: 25026 3.82 - 4.36: 30240 4.36 - 4.90: 43301 Nonbonded interactions: 110693 Sorted by model distance: nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.263 3.120 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.277 3.120 ... (remaining 110688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13676 Z= 0.340 Angle : 0.786 8.330 19730 Z= 0.459 Chirality : 0.060 0.566 2229 Planarity : 0.006 0.048 1479 Dihedral : 29.262 179.686 5879 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.42 % Allowed : 11.08 % Favored : 88.50 % 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: 1.05 (0.29), residues: 831 helix: 1.76 (0.22), residues: 541 sheet: -3.81 (0.82), residues: 12 loop : -1.27 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.006 0.002 HIS G 31 PHE 0.014 0.002 PHE A 78 TYR 0.010 0.002 TYR H 34 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8922 (m) cc_final: 0.8721 (t) outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.3924 time to fit residues: 77.0764 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN D 46 HIS E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.245 Angle : 0.588 9.784 19730 Z= 0.354 Chirality : 0.036 0.134 2229 Planarity : 0.004 0.038 1479 Dihedral : 31.118 162.999 4168 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.82 % Allowed : 12.76 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.29), residues: 831 helix: 2.12 (0.22), residues: 559 sheet: -2.30 (0.87), residues: 24 loop : -0.94 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.008 0.001 PHE H 62 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.3428 time to fit residues: 51.8042 Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13676 Z= 0.279 Angle : 0.585 9.058 19730 Z= 0.351 Chirality : 0.036 0.129 2229 Planarity : 0.004 0.042 1479 Dihedral : 30.805 164.075 4167 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 13.88 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.29), residues: 831 helix: 2.28 (0.22), residues: 559 sheet: -2.01 (0.95), residues: 23 loop : -0.98 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 82 HIS 0.006 0.001 HIS F 18 PHE 0.008 0.002 PHE H 62 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.8741 (tttt) cc_final: 0.8521 (tttt) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.3325 time to fit residues: 47.8693 Evaluate side-chains 101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 108 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.209 Angle : 0.553 8.836 19730 Z= 0.335 Chirality : 0.034 0.127 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.555 166.582 4165 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 14.17 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 831 helix: 2.48 (0.22), residues: 560 sheet: -1.65 (0.97), residues: 24 loop : -0.91 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.008 0.001 PHE A 67 TYR 0.008 0.001 TYR K 68 ARG 0.002 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.3330 time to fit residues: 47.5444 Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 35 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: C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.211 Angle : 0.553 8.606 19730 Z= 0.334 Chirality : 0.034 0.127 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.424 171.397 4165 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.54 % Allowed : 14.59 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.29), residues: 831 helix: 2.58 (0.22), residues: 561 sheet: -1.20 (1.01), residues: 24 loop : -0.82 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.008 0.001 PHE A 67 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.3395 time to fit residues: 49.6642 Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13676 Z= 0.340 Angle : 0.608 9.904 19730 Z= 0.361 Chirality : 0.038 0.130 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.589 170.840 4165 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.82 % Allowed : 14.87 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.29), residues: 831 helix: 2.41 (0.22), residues: 560 sheet: -1.49 (0.91), residues: 29 loop : -1.04 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.011 0.002 PHE K 44 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: F 95 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8642 (mtt-85) REVERT: G 77 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8560 (mtt180) REVERT: K 78 ASN cc_start: 0.5811 (p0) cc_final: 0.5584 (p0) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.3360 time to fit residues: 48.3202 Evaluate side-chains 106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.003 0.049 13676 Z= 0.191 Angle : 0.561 9.572 19730 Z= 0.338 Chirality : 0.035 0.126 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.424 171.374 4165 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.96 % Allowed : 15.01 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.29), residues: 831 helix: 2.58 (0.22), residues: 559 sheet: -1.04 (1.04), residues: 24 loop : -0.82 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.009 0.001 PHE K 44 TYR 0.009 0.001 TYR D 118 ARG 0.004 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: G 77 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (mtt180) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.3395 time to fit residues: 48.7672 Evaluate side-chains 106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13676 Z= 0.309 Angle : 0.597 9.582 19730 Z= 0.355 Chirality : 0.037 0.127 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.489 171.455 4165 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.12 % Allowed : 16.13 % Favored : 82.75 % 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: 2.19 (0.29), residues: 831 helix: 2.51 (0.22), residues: 559 sheet: -1.02 (1.06), residues: 24 loop : -0.83 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE H 62 TYR 0.011 0.001 TYR D 118 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.999 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.3304 time to fit residues: 45.1639 Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.204 Angle : 0.576 9.791 19730 Z= 0.346 Chirality : 0.035 0.126 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.458 171.819 4165 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.40 % Allowed : 15.85 % Favored : 82.75 % 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: 2.26 (0.29), residues: 831 helix: 2.56 (0.22), residues: 559 sheet: -0.99 (1.08), residues: 24 loop : -0.80 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR D 118 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.070 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.3304 time to fit residues: 45.2050 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.244 Angle : 0.576 9.997 19730 Z= 0.344 Chirality : 0.035 0.126 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.345 171.897 4165 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 15.71 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.29), residues: 831 helix: 2.60 (0.22), residues: 559 sheet: -0.87 (1.09), residues: 24 loop : -0.80 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE H 62 TYR 0.010 0.001 TYR D 118 ARG 0.004 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.071 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 100 average time/residue: 0.3289 time to fit residues: 44.5753 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0050 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.082441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053501 restraints weight = 37691.031| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.76 r_work: 0.2713 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.202 Angle : 0.570 10.030 19730 Z= 0.341 Chirality : 0.034 0.126 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.338 172.204 4165 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.98 % Allowed : 16.13 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.29), residues: 831 helix: 2.66 (0.22), residues: 559 sheet: -0.85 (1.09), residues: 24 loop : -0.72 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.009 0.001 PHE A 67 TYR 0.009 0.001 TYR D 118 ARG 0.002 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.93 seconds wall clock time: 49 minutes 16.54 seconds (2956.54 seconds total)