Starting phenix.real_space_refine on Fri Mar 15 22:21:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6g_29767/03_2024/8g6g_29767_updated.pdb" } resolution = 2.93 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= 0.002 sd= 0.022 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 314 5.49 5 S 13 5.16 5 C 7177 2.51 5 N 2427 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12985 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 803 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "K" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU K 73 " occ=0.63 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.63 residue: pdb=" N ARG K 74 " occ=0.73 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.73 Time building chain proxies: 6.96, per 1000 atoms: 0.54 Number of scatterers: 12985 At special positions: 0 Unit cell: (124.696, 93.304, 133.416, 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 314 15.00 O 3054 8.00 N 2427 7.00 C 7177 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 - 3.50 Amino acid : False - 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: 6.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 1 sheets defined 60.8% alpha, 1.2% beta 157 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.937A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.512A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.510A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.946A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing sheet with id= A, first strand: chain 'K' and resid 12 through 16 356 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 405 hydrogen bonds 810 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2444 1.33 - 1.45: 4527 1.45 - 1.57: 6232 1.57 - 1.69: 626 1.69 - 1.81: 24 Bond restraints: 13853 Sorted by residual: bond pdb=" P DA J 26 " pdb=" OP2 DA J 26 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" P DA J 16 " pdb=" OP2 DA J 16 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" P DC J -25 " pdb=" OP2 DC J -25 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" P DG J 27 " pdb=" OP2 DG J 27 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" P DG J 27 " pdb=" OP1 DG J 27 " ideal model delta sigma weight residual 1.480 1.514 -0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 13848 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.24: 1325 105.24 - 112.05: 7750 112.05 - 118.86: 3432 118.86 - 125.68: 6517 125.68 - 132.49: 1040 Bond angle restraints: 20064 Sorted by residual: angle pdb=" C3' DC J -26 " pdb=" O3' DC J -26 " pdb=" P DC J -25 " ideal model delta sigma weight residual 120.20 112.73 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DA J 16 " ideal model delta sigma weight residual 120.20 114.24 5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" C3' DT J 25 " pdb=" O3' DT J 25 " pdb=" P DA J 26 " ideal model delta sigma weight residual 120.20 114.49 5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" O3' DG J 27 " pdb=" P DA J 28 " pdb=" O5' DA J 28 " ideal model delta sigma weight residual 104.00 98.43 5.57 1.50e+00 4.44e-01 1.38e+01 angle pdb=" N MET K 1 " pdb=" CA MET K 1 " pdb=" C MET K 1 " ideal model delta sigma weight residual 111.00 100.99 10.01 2.80e+00 1.28e-01 1.28e+01 ... (remaining 20059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5934 35.90 - 71.80: 1566 71.80 - 107.70: 10 107.70 - 143.60: 3 143.60 - 179.50: 1 Dihedral angle restraints: 7514 sinusoidal: 5121 harmonic: 2393 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 40.50 179.50 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.90 131.10 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 90.72 129.28 1 3.50e+01 8.16e-04 1.28e+01 ... (remaining 7511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2242 0.095 - 0.191: 45 0.191 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.476: 5 Chirality restraints: 2292 Sorted by residual: chirality pdb=" P DC J -27 " pdb=" OP1 DC J -27 " pdb=" OP2 DC J -27 " pdb=" O5' DC J -27 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" P DA J 16 " pdb=" OP1 DA J 16 " pdb=" OP2 DA J 16 " pdb=" O5' DA J 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" P DC J -25 " pdb=" OP1 DC J -25 " pdb=" OP2 DC J -25 " pdb=" O5' DC J -25 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2289 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET K 1 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C MET K 1 " -0.038 2.00e-02 2.50e+03 pdb=" O MET K 1 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN K 2 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.023 2.00e-02 2.50e+03 1.02e-02 2.85e+00 pdb=" N9 DA I 57 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.023 2.00e-02 2.50e+03 9.73e-03 2.84e+00 pdb=" N9 DG I 26 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1893 2.77 - 3.30: 10497 3.30 - 3.84: 24505 3.84 - 4.37: 30026 4.37 - 4.90: 42863 Nonbonded interactions: 109784 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.238 2.520 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.263 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.290 2.440 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.303 2.520 ... (remaining 109779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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=0.63 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.210 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 42.540 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.003 0.045 13853 Z= 0.174 Angle : 0.567 10.009 20064 Z= 0.341 Chirality : 0.039 0.476 2292 Planarity : 0.004 0.039 1452 Dihedral : 28.343 179.500 5968 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.16 % Allowed : 22.79 % Favored : 76.05 % 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: 2.83 (0.29), residues: 801 helix: 2.78 (0.22), residues: 543 sheet: 1.47 (1.60), residues: 12 loop : -0.25 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR F 51 ARG 0.001 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.008 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 133 average time/residue: 1.9056 time to fit residues: 267.8489 Evaluate side-chains 132 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13853 Z= 0.368 Angle : 0.586 6.720 20064 Z= 0.356 Chirality : 0.038 0.154 2292 Planarity : 0.005 0.042 1452 Dihedral : 30.286 178.484 4352 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.48 % Allowed : 20.46 % Favored : 76.05 % 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: 2.38 (0.29), residues: 801 helix: 2.45 (0.22), residues: 543 sheet: 0.89 (1.53), residues: 12 loop : -0.43 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.010 0.002 PHE D 67 TYR 0.011 0.002 TYR A 54 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.079 Fit side-chains REVERT: B 95 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8025 (mtt-85) REVERT: C 73 ASN cc_start: 0.8110 (t160) cc_final: 0.7847 (t160) outliers start: 24 outliers final: 9 residues processed: 144 average time/residue: 1.9836 time to fit residues: 301.8690 Evaluate side-chains 142 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 3 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13853 Z= 0.304 Angle : 0.578 10.370 20064 Z= 0.351 Chirality : 0.036 0.138 2292 Planarity : 0.004 0.042 1452 Dihedral : 30.303 178.510 4346 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 22.35 % Favored : 74.60 % 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: 2.36 (0.29), residues: 801 helix: 2.45 (0.22), residues: 543 sheet: 0.66 (1.54), residues: 12 loop : -0.44 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.002 PHE B 61 TYR 0.011 0.002 TYR E 54 ARG 0.002 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.037 Fit side-chains REVERT: A 120 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8520 (mtt) REVERT: B 95 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7990 (mtt-85) REVERT: C 73 ASN cc_start: 0.8097 (t160) cc_final: 0.7816 (t160) REVERT: F 93 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7158 (mp10) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 2.0068 time to fit residues: 292.2600 Evaluate side-chains 147 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13853 Z= 0.212 Angle : 0.550 7.269 20064 Z= 0.338 Chirality : 0.034 0.130 2292 Planarity : 0.004 0.040 1452 Dihedral : 30.308 178.441 4346 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.19 % Allowed : 22.06 % Favored : 74.75 % 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: 2.53 (0.29), residues: 801 helix: 2.57 (0.22), residues: 543 sheet: 0.84 (1.53), residues: 12 loop : -0.36 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.009 0.001 PHE F 61 TYR 0.010 0.001 TYR F 51 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.064 Fit side-chains REVERT: A 120 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8483 (mtt) REVERT: C 73 ASN cc_start: 0.8080 (t160) cc_final: 0.7789 (t160) REVERT: F 93 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7149 (mp10) outliers start: 22 outliers final: 14 residues processed: 140 average time/residue: 1.9268 time to fit residues: 285.0404 Evaluate side-chains 148 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13853 Z= 0.296 Angle : 0.557 6.198 20064 Z= 0.340 Chirality : 0.035 0.143 2292 Planarity : 0.004 0.041 1452 Dihedral : 30.235 178.378 4346 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.48 % Allowed : 21.63 % Favored : 74.89 % 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: 2.48 (0.29), residues: 801 helix: 2.55 (0.22), residues: 543 sheet: 0.80 (1.56), residues: 12 loop : -0.43 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.009 0.002 PHE B 61 TYR 0.012 0.002 TYR E 54 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.989 Fit side-chains REVERT: C 36 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7969 (mtpp) REVERT: C 73 ASN cc_start: 0.8085 (t160) cc_final: 0.7853 (t160) REVERT: E 131 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7612 (mtp85) REVERT: H 60 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8431 (m-40) outliers start: 24 outliers final: 12 residues processed: 139 average time/residue: 1.9887 time to fit residues: 291.7025 Evaluate side-chains 145 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13853 Z= 0.207 Angle : 0.529 5.435 20064 Z= 0.327 Chirality : 0.033 0.127 2292 Planarity : 0.004 0.039 1452 Dihedral : 30.224 179.044 4346 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.89 % Allowed : 23.66 % Favored : 74.46 % 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: 2.67 (0.29), residues: 801 helix: 2.67 (0.22), residues: 543 sheet: 0.86 (1.55), residues: 12 loop : -0.29 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR F 51 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.920 Fit side-chains REVERT: C 73 ASN cc_start: 0.8042 (t160) cc_final: 0.7813 (t160) REVERT: E 131 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7595 (mtp85) REVERT: F 93 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7306 (mp10) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 2.0451 time to fit residues: 291.8154 Evaluate side-chains 137 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13853 Z= 0.173 Angle : 0.522 5.042 20064 Z= 0.324 Chirality : 0.032 0.127 2292 Planarity : 0.004 0.038 1452 Dihedral : 30.215 179.138 4346 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.03 % Allowed : 23.95 % Favored : 74.02 % 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: 2.72 (0.29), residues: 801 helix: 2.70 (0.22), residues: 543 sheet: 0.88 (1.55), residues: 12 loop : -0.26 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.010 0.001 TYR F 51 ARG 0.002 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.955 Fit side-chains REVERT: C 73 ASN cc_start: 0.8028 (t160) cc_final: 0.7798 (t160) REVERT: E 131 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7581 (mtp85) REVERT: F 93 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: K 1 MET cc_start: 0.2603 (tmm) cc_final: 0.2308 (pmm) outliers start: 14 outliers final: 10 residues processed: 135 average time/residue: 2.0187 time to fit residues: 287.5833 Evaluate side-chains 138 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13853 Z= 0.411 Angle : 0.607 6.473 20064 Z= 0.368 Chirality : 0.039 0.162 2292 Planarity : 0.005 0.042 1452 Dihedral : 30.353 177.680 4346 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 23.22 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.29), residues: 801 helix: 2.32 (0.22), residues: 543 sheet: 0.53 (1.33), residues: 17 loop : -0.50 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.011 0.002 PHE A 84 TYR 0.015 0.002 TYR E 54 ARG 0.003 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.962 Fit side-chains REVERT: C 73 ASN cc_start: 0.8156 (t160) cc_final: 0.7910 (t160) REVERT: C 92 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: E 131 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7615 (mtp85) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 1.9868 time to fit residues: 284.7911 Evaluate side-chains 139 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13853 Z= 0.287 Angle : 0.580 10.742 20064 Z= 0.352 Chirality : 0.036 0.141 2292 Planarity : 0.004 0.041 1452 Dihedral : 30.350 177.918 4346 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.90 % Allowed : 23.22 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.29), residues: 801 helix: 2.41 (0.22), residues: 543 sheet: 0.78 (1.37), residues: 17 loop : -0.46 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.002 PHE F 61 TYR 0.012 0.002 TYR E 54 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.077 Fit side-chains REVERT: C 73 ASN cc_start: 0.8122 (t160) cc_final: 0.7873 (t160) REVERT: E 131 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7713 (mtp85) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 2.0565 time to fit residues: 303.7246 Evaluate side-chains 142 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13853 Z= 0.202 Angle : 0.568 12.874 20064 Z= 0.344 Chirality : 0.034 0.241 2292 Planarity : 0.004 0.040 1452 Dihedral : 30.342 178.216 4346 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.74 % Allowed : 24.38 % Favored : 73.88 % 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: 2.53 (0.29), residues: 801 helix: 2.57 (0.22), residues: 543 sheet: 0.60 (1.38), residues: 17 loop : -0.36 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.011 0.001 TYR F 51 ARG 0.001 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.139 Fit side-chains REVERT: C 73 ASN cc_start: 0.8075 (t160) cc_final: 0.7827 (t160) REVERT: E 131 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7755 (mtp85) outliers start: 12 outliers final: 10 residues processed: 139 average time/residue: 2.0222 time to fit residues: 296.4429 Evaluate side-chains 142 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.161142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135047 restraints weight = 13536.899| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 0.76 r_work: 0.3437 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13853 Z= 0.217 Angle : 0.549 7.003 20064 Z= 0.336 Chirality : 0.034 0.136 2292 Planarity : 0.004 0.040 1452 Dihedral : 30.307 179.188 4346 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.18 % Allowed : 23.80 % Favored : 74.02 % 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: 2.63 (0.29), residues: 801 helix: 2.64 (0.22), residues: 543 sheet: 0.74 (1.36), residues: 17 loop : -0.30 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR F 51 ARG 0.001 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4679.41 seconds wall clock time: 82 minutes 58.90 seconds (4978.90 seconds total)