Starting phenix.real_space_refine on Thu Nov 14 00:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwi_60528/11_2024/8zwi_60528.cif" } resolution = 3.0 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: 3 Type Number sf(0) Gaussians C 1590 2.51 5 N 438 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2526 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.68, per 1000 atoms: 0.67 Number of scatterers: 2526 At special positions: 0 Unit cell: (97.11, 73.87, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 498 8.00 N 438 7.00 C 1590 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: 0.61 Conformation dependent library (CDL) restraints added in 338.5 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.549A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 58 removed outlier: 6.792A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLY E 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS A 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ALA E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU E 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.435A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72 removed outlier: 6.342A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 82 removed outlier: 5.710A pdb=" N THR A 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ALA D 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS D 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL D 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92 removed outlier: 6.900A pdb=" N ILE D 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.549A pdb=" N TYR F 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 58 removed outlier: 6.791A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU F 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL C 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N VAL F 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N GLY C 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS F 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ALA C 53 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR F 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLU C 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA F 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.435A pdb=" N VAL F 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN F 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.343A pdb=" N VAL F 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 82 removed outlier: 5.711A pdb=" N THR F 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA B 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS B 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN F 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR F 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA F 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.900A pdb=" N ILE B 88 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE F 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 432 1.28 - 1.35: 390 1.35 - 1.41: 101 1.41 - 1.48: 451 1.48 - 1.54: 1164 Bond restraints: 2538 Sorted by residual: bond pdb=" C ILE F 88 " pdb=" N ALA F 89 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" C ILE A 88 " pdb=" N ALA A 89 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" C ILE D 88 " pdb=" N ALA D 89 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.29e-02 6.01e+03 2.22e+00 ... (remaining 2533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3019 1.18 - 2.35: 324 2.35 - 3.53: 77 3.53 - 4.71: 0 4.71 - 5.88: 12 Bond angle restraints: 3432 Sorted by residual: angle pdb=" OG1 THR E 44 " pdb=" CB THR E 44 " pdb=" CG2 THR E 44 " ideal model delta sigma weight residual 109.30 103.98 5.32 2.00e+00 2.50e-01 7.09e+00 angle pdb=" OG1 THR F 44 " pdb=" CB THR F 44 " pdb=" CG2 THR F 44 " ideal model delta sigma weight residual 109.30 103.99 5.31 2.00e+00 2.50e-01 7.05e+00 angle pdb=" OG1 THR A 44 " pdb=" CB THR A 44 " pdb=" CG2 THR A 44 " ideal model delta sigma weight residual 109.30 104.00 5.30 2.00e+00 2.50e-01 7.03e+00 angle pdb=" OG1 THR D 44 " pdb=" CB THR D 44 " pdb=" CG2 THR D 44 " ideal model delta sigma weight residual 109.30 104.02 5.28 2.00e+00 2.50e-01 6.96e+00 angle pdb=" OG1 THR C 44 " pdb=" CB THR C 44 " pdb=" CG2 THR C 44 " ideal model delta sigma weight residual 109.30 104.03 5.27 2.00e+00 2.50e-01 6.95e+00 ... (remaining 3427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.96: 1209 8.96 - 17.92: 171 17.92 - 26.88: 72 26.88 - 35.84: 24 35.84 - 44.79: 6 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA LYS C 80 " pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " pdb=" CD LYS C 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.26 34.74 3 1.50e+01 4.44e-03 5.91e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.26 34.74 3 1.50e+01 4.44e-03 5.90e+00 dihedral pdb=" CA LYS E 80 " pdb=" CB LYS E 80 " pdb=" CG LYS E 80 " pdb=" CD LYS E 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.27 34.73 3 1.50e+01 4.44e-03 5.90e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 212 0.037 - 0.074: 104 0.074 - 0.111: 115 0.111 - 0.148: 17 0.148 - 0.186: 8 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR F 75 " pdb=" CA THR F 75 " pdb=" OG1 THR F 75 " pdb=" CG2 THR F 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR D 75 " pdb=" CA THR D 75 " pdb=" OG1 THR D 75 " pdb=" CG2 THR D 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB THR E 75 " pdb=" CA THR E 75 " pdb=" OG1 THR E 75 " pdb=" CG2 THR E 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 453 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.76e+00 pdb=" CG HIS C 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.74e+00 pdb=" CG HIS F 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.73e+00 pdb=" CG HIS B 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.004 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 537 2.79 - 3.32: 2199 3.32 - 3.84: 3791 3.84 - 4.37: 4168 4.37 - 4.90: 8897 Nonbonded interactions: 19592 Sorted by model distance: nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.262 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.262 3.120 ... (remaining 19587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.011 0.048 2538 Z= 0.781 Angle : 0.859 5.881 3432 Z= 0.499 Chirality : 0.065 0.186 456 Planarity : 0.003 0.011 420 Dihedral : 11.260 44.795 858 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -3.70 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS C 50 PHE 0.013 0.004 PHE B 94 TYR 0.005 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.4191 time to fit residues: 55.1419 Evaluate side-chains 22 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.132 Angle : 0.447 4.646 3432 Z= 0.245 Chirality : 0.052 0.126 456 Planarity : 0.001 0.006 420 Dihedral : 3.475 9.489 366 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.16 % Allowed : 8.91 % Favored : 89.92 % 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: -2.79 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.006 0.002 PHE B 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.287 Fit side-chains REVERT: F 75 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8303 (t) REVERT: C 60 LYS cc_start: 0.7905 (tttt) cc_final: 0.7661 (tttp) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 1.3201 time to fit residues: 39.3308 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2538 Z= 0.257 Angle : 0.467 3.078 3432 Z= 0.267 Chirality : 0.050 0.122 456 Planarity : 0.002 0.006 420 Dihedral : 3.692 10.588 366 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.33 % Allowed : 10.85 % Favored : 86.82 % 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: -2.42 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 50 PHE 0.007 0.002 PHE A 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.268 Fit side-chains REVERT: E 60 LYS cc_start: 0.7972 (tttt) cc_final: 0.7714 (tttp) REVERT: F 75 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8274 (t) REVERT: B 75 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8264 (t) REVERT: C 60 LYS cc_start: 0.8014 (tttt) cc_final: 0.7673 (tttp) outliers start: 6 outliers final: 1 residues processed: 24 average time/residue: 0.8842 time to fit residues: 22.1508 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.130 Angle : 0.390 2.729 3432 Z= 0.224 Chirality : 0.050 0.122 456 Planarity : 0.001 0.005 420 Dihedral : 3.260 9.275 366 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % 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: -2.13 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 PHE 0.005 0.001 PHE B 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.292 Fit side-chains REVERT: F 75 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8214 (t) REVERT: B 75 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8244 (t) REVERT: C 60 LYS cc_start: 0.7943 (tttt) cc_final: 0.7634 (tttp) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 1.2439 time to fit residues: 30.8189 Evaluate side-chains 22 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2538 Z= 0.511 Angle : 0.578 3.145 3432 Z= 0.334 Chirality : 0.053 0.124 456 Planarity : 0.002 0.008 420 Dihedral : 4.209 11.050 366 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.55 % Allowed : 16.28 % Favored : 82.17 % 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: -2.27 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS D 50 PHE 0.011 0.003 PHE F 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.269 Fit side-chains REVERT: D 75 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8401 (t) REVERT: F 75 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8240 (t) REVERT: B 75 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8245 (t) REVERT: C 60 LYS cc_start: 0.7976 (tttt) cc_final: 0.7640 (tttp) outliers start: 4 outliers final: 0 residues processed: 26 average time/residue: 1.0780 time to fit residues: 28.9943 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2538 Z= 0.231 Angle : 0.442 2.436 3432 Z= 0.256 Chirality : 0.050 0.122 456 Planarity : 0.001 0.005 420 Dihedral : 3.716 10.352 366 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.16 % Allowed : 16.67 % Favored : 82.17 % 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: -2.08 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 50 PHE 0.008 0.002 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.309 Fit side-chains REVERT: F 75 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8292 (t) REVERT: B 75 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8302 (t) REVERT: C 60 LYS cc_start: 0.7983 (tttt) cc_final: 0.7590 (tttp) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 1.1186 time to fit residues: 24.4038 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2538 Z= 0.172 Angle : 0.409 2.282 3432 Z= 0.236 Chirality : 0.050 0.121 456 Planarity : 0.001 0.005 420 Dihedral : 3.459 10.821 366 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 17.83 % Favored : 80.62 % 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: -1.88 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.006 0.002 PHE A 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.280 Fit side-chains REVERT: E 60 LYS cc_start: 0.7967 (tttp) cc_final: 0.7692 (tptm) REVERT: F 75 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 75 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8273 (t) REVERT: C 60 LYS cc_start: 0.7913 (tttt) cc_final: 0.7523 (tttp) outliers start: 4 outliers final: 1 residues processed: 20 average time/residue: 1.1184 time to fit residues: 23.1931 Evaluate side-chains 21 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2538 Z= 0.302 Angle : 0.489 3.678 3432 Z= 0.280 Chirality : 0.050 0.121 456 Planarity : 0.002 0.009 420 Dihedral : 3.815 10.480 366 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 17.83 % Favored : 80.62 % 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 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.009 0.002 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.279 Fit side-chains REVERT: F 75 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (t) REVERT: B 75 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8299 (t) REVERT: C 60 LYS cc_start: 0.7945 (tttt) cc_final: 0.7641 (tttp) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 1.0243 time to fit residues: 24.4932 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2538 Z= 0.245 Angle : 0.460 3.365 3432 Z= 0.264 Chirality : 0.050 0.122 456 Planarity : 0.002 0.008 420 Dihedral : 3.719 10.974 366 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.55 % Allowed : 17.44 % Favored : 81.01 % 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: -1.89 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.273 Fit side-chains REVERT: D 83 GLU cc_start: 0.7784 (tt0) cc_final: 0.7551 (tt0) REVERT: E 60 LYS cc_start: 0.7907 (tttp) cc_final: 0.7544 (tttm) REVERT: F 75 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 75 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8309 (t) REVERT: C 60 LYS cc_start: 0.7896 (tttt) cc_final: 0.7606 (tttp) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 1.1041 time to fit residues: 29.6816 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2538 Z= 0.408 Angle : 0.555 3.877 3432 Z= 0.317 Chirality : 0.051 0.126 456 Planarity : 0.002 0.011 420 Dihedral : 4.134 11.722 366 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 17.05 % Favored : 81.01 % 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: -2.05 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS D 50 PHE 0.011 0.003 PHE A 94 TYR 0.005 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.283 Fit side-chains REVERT: D 75 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8450 (t) REVERT: D 83 GLU cc_start: 0.7809 (tt0) cc_final: 0.7574 (tt0) REVERT: F 75 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (t) REVERT: B 62 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: B 75 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8306 (t) REVERT: B 83 GLU cc_start: 0.7804 (tt0) cc_final: 0.7583 (tt0) REVERT: C 60 LYS cc_start: 0.7950 (tttt) cc_final: 0.7616 (tttp) outliers start: 5 outliers final: 0 residues processed: 28 average time/residue: 1.2401 time to fit residues: 35.7697 Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.166874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.137672 restraints weight = 2919.206| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.37 r_work: 0.3842 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 2538 Z= 0.513 Angle : 1.475 59.179 3432 Z= 0.886 Chirality : 0.051 0.130 456 Planarity : 0.002 0.020 420 Dihedral : 4.104 11.738 366 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.71 % Allowed : 17.05 % Favored : 80.23 % 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: -2.07 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.010 0.002 PHE A 94 TYR 0.005 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.69 seconds wall clock time: 24 minutes 1.13 seconds (1441.13 seconds total)