Starting phenix.real_space_refine on Sun Nov 17 01:18:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzy_33534/11_2024/7xzy_33534.cif" } resolution = 3.97 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= 0.003 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 330 5.49 5 S 14 5.16 5 C 7015 2.51 5 N 2417 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3372 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3393 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Time building chain proxies: 6.97, per 1000 atoms: 0.54 Number of scatterers: 12821 At special positions: 0 Unit cell: (127.6, 151.8, 105.6, 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 14 16.00 P 330 15.00 O 3045 8.00 N 2417 7.00 C 7015 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: 3.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 163 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.345A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.175A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.127A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.536A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.152A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.306A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 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 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.699A 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 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.222A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.639A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.555A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.735A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 410 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 842 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 3.85 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: 2094 1.33 - 1.45: 4796 1.45 - 1.57: 6152 1.57 - 1.69: 658 1.69 - 1.81: 24 Bond restraints: 13724 Sorted by residual: bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ASN H 81 " pdb=" CA ASN H 81 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.21e+00 bond pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N ILE D 66 " pdb=" CA ILE D 66 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.21e+00 bond pdb=" N LYS C 118 " pdb=" CA LYS C 118 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.23e-02 6.61e+03 4.51e+00 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 19164 1.62 - 3.24: 711 3.24 - 4.87: 51 4.87 - 6.49: 15 6.49 - 8.11: 7 Bond angle restraints: 19948 Sorted by residual: angle pdb=" CA ILE D 66 " pdb=" C ILE D 66 " pdb=" O ILE D 66 " ideal model delta sigma weight residual 121.17 117.11 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.00 3.42 9.60e-01 1.09e+00 1.27e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" CA GLU A 73 " pdb=" CB GLU A 73 " pdb=" CG GLU A 73 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" C ALA C 86 " pdb=" N ILE C 87 " pdb=" CA ILE C 87 " ideal model delta sigma weight residual 120.56 116.25 4.31 1.28e+00 6.10e-01 1.14e+01 ... (remaining 19943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4731 17.96 - 35.91: 1186 35.91 - 53.87: 1116 53.87 - 71.82: 317 71.82 - 89.78: 23 Dihedral angle restraints: 7373 sinusoidal: 5169 harmonic: 2204 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 124.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.82 -41.18 2 1.50e+01 4.44e-03 9.25e+00 ... (remaining 7370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2042 0.061 - 0.123: 209 0.123 - 0.184: 10 0.184 - 0.245: 1 0.245 - 0.306: 2 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2261 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C ASN B 64 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN B 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C LEU B 62 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 69 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ALA B 69 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 69 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 70 " -0.014 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 199 2.63 - 3.20: 10916 3.20 - 3.76: 24685 3.76 - 4.33: 30688 4.33 - 4.90: 43141 Nonbonded interactions: 109629 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.062 3.040 nonbonded pdb=" O ARG C 20 " pdb=" NZ LYS D 117 " model vdw 2.080 3.120 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 105 " model vdw 2.136 3.040 nonbonded pdb=" O2 DC I 73 " pdb=" N2 DG J 121 " model vdw 2.162 2.496 nonbonded pdb=" NH2 ARG H 30 " pdb=" OP2 DA I 146 " model vdw 2.222 3.120 ... (remaining 109624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 31.620 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 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:3.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13724 Z= 0.227 Angle : 0.688 8.112 19948 Z= 0.424 Chirality : 0.039 0.306 2264 Planarity : 0.005 0.039 1381 Dihedral : 27.844 89.778 5953 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.06 % 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: 1.04 (0.28), residues: 746 helix: 1.20 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.018 0.002 PHE G 25 TYR 0.023 0.002 TYR C 50 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.054 Fit side-chains REVERT: A 60 LEU cc_start: 0.9316 (mp) cc_final: 0.9116 (mp) REVERT: B 59 LYS cc_start: 0.8792 (tttm) cc_final: 0.8221 (tttm) REVERT: B 63 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7947 (mp0) REVERT: C 64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8299 (mm-30) REVERT: C 92 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7633 (mt-10) REVERT: G 39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7231 (m-80) REVERT: G 92 GLU cc_start: 0.8786 (mp0) cc_final: 0.8585 (mp0) REVERT: H 31 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7980 (mmmt) REVERT: H 73 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2565 time to fit residues: 67.4944 Evaluate side-chains 144 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 75 HIS D 81 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13724 Z= 0.181 Angle : 0.576 6.620 19948 Z= 0.342 Chirality : 0.034 0.152 2264 Planarity : 0.005 0.051 1381 Dihedral : 31.131 89.050 4432 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 9.45 % Favored : 87.72 % 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: 2.11 (0.30), residues: 746 helix: 2.07 (0.21), residues: 552 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.018 0.001 PHE E 67 TYR 0.017 0.002 TYR F 88 ARG 0.006 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.964 Fit side-chains REVERT: A 73 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 73 THR cc_start: 0.9209 (m) cc_final: 0.8832 (t) REVERT: E 67 PHE cc_start: 0.8591 (t80) cc_final: 0.8332 (t80) REVERT: F 93 GLN cc_start: 0.8503 (tp40) cc_final: 0.8204 (tp40) REVERT: G 33 LEU cc_start: 0.9057 (mm) cc_final: 0.8812 (mm) REVERT: G 92 GLU cc_start: 0.8861 (mp0) cc_final: 0.8525 (mp0) REVERT: H 39 TYR cc_start: 0.8362 (t80) cc_final: 0.7903 (t80) REVERT: H 42 LEU cc_start: 0.9517 (tp) cc_final: 0.9234 (tp) REVERT: H 65 ASP cc_start: 0.8656 (t70) cc_final: 0.8397 (t0) outliers start: 18 outliers final: 3 residues processed: 177 average time/residue: 0.2254 time to fit residues: 59.1866 Evaluate side-chains 143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 59 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 0.0060 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 60 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13724 Z= 0.352 Angle : 0.831 18.006 19948 Z= 0.474 Chirality : 0.043 0.262 2264 Planarity : 0.007 0.070 1381 Dihedral : 32.052 98.902 4432 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.31 % Allowed : 14.17 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.04 (0.29), residues: 746 helix: 1.37 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 113 PHE 0.009 0.002 PHE B 61 TYR 0.020 0.003 TYR D 37 ARG 0.012 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.8688 (t0) cc_final: 0.8477 (t0) REVERT: C 75 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8289 (mmmm) REVERT: D 98 LEU cc_start: 0.9380 (mm) cc_final: 0.9127 (mt) REVERT: E 59 GLU cc_start: 0.8228 (pm20) cc_final: 0.7924 (pm20) REVERT: F 63 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: G 101 THR cc_start: 0.9217 (m) cc_final: 0.8910 (t) REVERT: H 54 LYS cc_start: 0.9253 (mmtp) cc_final: 0.9048 (mmmm) REVERT: H 56 MET cc_start: 0.9390 (mmm) cc_final: 0.8964 (tpp) REVERT: H 81 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8558 (t0) outliers start: 21 outliers final: 11 residues processed: 173 average time/residue: 0.3012 time to fit residues: 72.6341 Evaluate side-chains 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.0070 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.8710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13724 Z= 0.195 Angle : 0.615 13.276 19948 Z= 0.359 Chirality : 0.034 0.145 2264 Planarity : 0.004 0.051 1381 Dihedral : 31.481 92.708 4432 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 19.53 % Favored : 78.58 % 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: 2.01 (0.30), residues: 746 helix: 2.24 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.018 0.001 TYR D 37 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 GLU cc_start: 0.8181 (mp0) cc_final: 0.7914 (mp0) REVERT: E 59 GLU cc_start: 0.8012 (pm20) cc_final: 0.7688 (pm20) REVERT: G 92 GLU cc_start: 0.8781 (mp0) cc_final: 0.8497 (pm20) REVERT: H 81 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7763 (t0) outliers start: 12 outliers final: 5 residues processed: 138 average time/residue: 0.2721 time to fit residues: 52.7257 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.9030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13724 Z= 0.182 Angle : 0.580 8.315 19948 Z= 0.342 Chirality : 0.032 0.151 2264 Planarity : 0.004 0.050 1381 Dihedral : 31.172 89.854 4432 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.73 % Allowed : 21.57 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.31), residues: 746 helix: 2.57 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.017 0.001 TYR D 37 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.7951 (pm20) cc_final: 0.7623 (pm20) REVERT: G 50 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: H 31 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8240 (mmmt) REVERT: H 51 ILE cc_start: 0.8121 (mm) cc_final: 0.7831 (tp) outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 0.2580 time to fit residues: 48.3141 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 50 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.0010 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 1.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13724 Z= 0.245 Angle : 0.660 15.675 19948 Z= 0.379 Chirality : 0.035 0.150 2264 Planarity : 0.004 0.046 1381 Dihedral : 31.225 89.941 4432 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.15 % Allowed : 22.20 % Favored : 74.65 % 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 (0.31), residues: 746 helix: 2.32 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.013 0.001 PHE C 25 TYR 0.025 0.002 TYR D 37 ARG 0.005 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8328 (tptm) cc_final: 0.7935 (tppt) REVERT: C 56 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8213 (mm-30) REVERT: D 90 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: E 59 GLU cc_start: 0.7995 (pm20) cc_final: 0.7738 (pm20) REVERT: F 50 ILE cc_start: 0.8579 (mm) cc_final: 0.7953 (mm) REVERT: F 53 GLU cc_start: 0.8168 (mp0) cc_final: 0.7732 (mp0) REVERT: H 73 GLU cc_start: 0.8725 (tp30) cc_final: 0.8525 (tp30) outliers start: 20 outliers final: 11 residues processed: 135 average time/residue: 0.2772 time to fit residues: 53.1233 Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 1.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13724 Z= 0.232 Angle : 0.628 13.874 19948 Z= 0.362 Chirality : 0.034 0.173 2264 Planarity : 0.004 0.049 1381 Dihedral : 31.002 89.922 4432 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 25.20 % Favored : 72.60 % 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 (0.31), residues: 746 helix: 2.47 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 79 PHE 0.007 0.001 PHE E 67 TYR 0.016 0.001 TYR F 88 ARG 0.003 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8143 (mm-30) REVERT: D 44 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8953 (tm-30) REVERT: E 59 GLU cc_start: 0.8101 (pm20) cc_final: 0.7798 (pm20) REVERT: F 91 LYS cc_start: 0.9358 (tttt) cc_final: 0.9060 (tttt) REVERT: H 31 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8112 (mmmt) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.2533 time to fit residues: 46.1631 Evaluate side-chains 121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 1.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13724 Z= 0.239 Angle : 0.645 11.276 19948 Z= 0.373 Chirality : 0.034 0.158 2264 Planarity : 0.004 0.049 1381 Dihedral : 30.887 89.756 4432 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.05 % Allowed : 26.46 % Favored : 71.50 % 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: 2.08 (0.31), residues: 746 helix: 2.33 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 79 PHE 0.008 0.001 PHE E 67 TYR 0.020 0.002 TYR F 88 ARG 0.005 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8126 (mm-30) REVERT: D 44 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8938 (tm-30) REVERT: D 81 ASN cc_start: 0.9147 (t0) cc_final: 0.8799 (t0) REVERT: E 59 GLU cc_start: 0.7963 (pm20) cc_final: 0.7710 (pm20) REVERT: F 53 GLU cc_start: 0.7883 (mp0) cc_final: 0.7655 (mp0) REVERT: F 91 LYS cc_start: 0.9429 (tttt) cc_final: 0.9214 (tttt) REVERT: H 90 GLU cc_start: 0.8796 (pm20) cc_final: 0.8459 (pm20) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.2672 time to fit residues: 46.4502 Evaluate side-chains 118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 1.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13724 Z= 0.260 Angle : 0.681 16.608 19948 Z= 0.387 Chirality : 0.035 0.182 2264 Planarity : 0.004 0.049 1381 Dihedral : 30.836 89.036 4432 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.57 % Allowed : 27.72 % Favored : 70.71 % 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: 2.15 (0.32), residues: 746 helix: 2.42 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.53 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.053 0.002 TYR D 80 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8091 (mm-30) REVERT: D 44 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8920 (tm-30) REVERT: E 59 GLU cc_start: 0.8072 (pm20) cc_final: 0.7800 (pm20) REVERT: F 91 LYS cc_start: 0.9411 (tttt) cc_final: 0.9179 (tttt) outliers start: 10 outliers final: 6 residues processed: 114 average time/residue: 0.2567 time to fit residues: 42.1178 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 1.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13724 Z= 0.256 Angle : 0.674 16.601 19948 Z= 0.385 Chirality : 0.034 0.172 2264 Planarity : 0.004 0.048 1381 Dihedral : 30.756 89.299 4432 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.73 % Allowed : 27.56 % Favored : 70.71 % 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: 2.06 (0.32), residues: 746 helix: 2.36 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.57 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE E 84 TYR 0.035 0.002 TYR D 80 ARG 0.003 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 57 SER cc_start: 0.9027 (t) cc_final: 0.8362 (p) REVERT: C 56 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8117 (mm-30) REVERT: D 44 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8922 (tm-30) REVERT: E 59 GLU cc_start: 0.7992 (pm20) cc_final: 0.7734 (pm20) REVERT: E 81 ASP cc_start: 0.8668 (p0) cc_final: 0.8089 (p0) REVERT: F 91 LYS cc_start: 0.9428 (tttt) cc_final: 0.9171 (tttt) REVERT: H 90 GLU cc_start: 0.8804 (pm20) cc_final: 0.8539 (pm20) outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 0.2516 time to fit residues: 42.2854 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 40.0000 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.039342 restraints weight = 84414.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.040131 restraints weight = 45482.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.040716 restraints weight = 31287.815| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 1.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13724 Z= 0.258 Angle : 0.683 16.439 19948 Z= 0.389 Chirality : 0.034 0.172 2264 Planarity : 0.004 0.048 1381 Dihedral : 30.748 88.946 4432 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.57 % Allowed : 27.87 % Favored : 70.55 % 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: 1.98 (0.32), residues: 746 helix: 2.35 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.030 0.002 TYR F 88 ARG 0.003 0.000 ARG H 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.44 seconds wall clock time: 45 minutes 13.41 seconds (2713.41 seconds total)