Starting phenix.real_space_refine on Thu Sep 26 02:58:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/09_2024/6vwj_21418.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3802 2.51 5 N 1044 2.21 5 O 1122 1.98 5 H 5789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3865 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7934 Classifications: {'peptide': 507} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 471} Chain breaks: 4 Time building chain proxies: 6.94, per 1000 atoms: 0.59 Number of scatterers: 11799 At special positions: 0 Unit cell: (92.22, 113.42, 103.88, 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 42 16.00 O 1122 8.00 N 1044 7.00 C 3802 6.00 H 5789 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 973.5 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 12.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.725A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 15 through 22 removed outlier: 4.349A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.749A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.346A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.999A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.800A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 875 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP A 886 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA A 877 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.691A pdb=" N ILE B 76 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.840A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 85 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B 112 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 87 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLU B 114 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 89 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 209 removed outlier: 4.097A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 248 removed outlier: 8.084A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB5, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.145A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 747 through 751 Processing sheet with id=AB7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5789 1.03 - 1.23: 471 1.23 - 1.44: 2236 1.44 - 1.64: 3410 1.64 - 1.84: 50 Bond restraints: 11956 Sorted by residual: bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL A 580 " pdb=" H VAL A 580 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB LYS A 897 " pdb=" CG LYS A 897 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB CYS A 785 " pdb=" SG CYS A 785 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 11951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 20600 1.70 - 3.40: 842 3.40 - 5.10: 89 5.10 - 6.80: 21 6.80 - 8.50: 1 Bond angle restraints: 21553 Sorted by residual: angle pdb=" N ASN B 11 " pdb=" CA ASN B 11 " pdb=" C ASN B 11 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 angle pdb=" CA LYS B 600 " pdb=" CB LYS B 600 " pdb=" CG LYS B 600 " ideal model delta sigma weight residual 114.10 107.58 6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N ASP B 12 " pdb=" CA ASP B 12 " pdb=" C ASP B 12 " ideal model delta sigma weight residual 109.06 114.51 -5.45 1.70e+00 3.46e-01 1.03e+01 angle pdb=" CA TYR A 628 " pdb=" CB TYR A 628 " pdb=" CG TYR A 628 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " pdb=" CG LYS A 862 " ideal model delta sigma weight residual 114.10 107.84 6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 21548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5204 17.48 - 34.96: 344 34.96 - 52.45: 111 52.45 - 69.93: 84 69.93 - 87.41: 7 Dihedral angle restraints: 5750 sinusoidal: 3133 harmonic: 2617 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -145.73 59.73 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CA SER B 788 " pdb=" C SER B 788 " pdb=" N ASN B 789 " pdb=" CA ASN B 789 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER A 788 " pdb=" C SER A 788 " pdb=" N ASN A 789 " pdb=" CA ASN A 789 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 456 0.035 - 0.070: 245 0.070 - 0.105: 110 0.105 - 0.140: 52 0.140 - 0.175: 11 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 871 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 112 " -0.099 9.50e-02 1.11e+02 4.89e-02 3.05e+01 pdb=" NE ARG B 112 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 112 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG B 112 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 112 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 112 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 112 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 865 " 0.032 9.50e-02 1.11e+02 3.24e-02 2.12e+01 pdb=" NE ARG A 865 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 865 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 865 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 865 " 0.041 2.00e-02 2.50e+03 pdb="HH11 ARG A 865 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 865 " 0.027 2.00e-02 2.50e+03 pdb="HH21 ARG A 865 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 865 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 269 " -0.001 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" CG HIS B 269 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS B 269 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 269 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS B 269 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 269 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS B 269 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS B 269 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS B 269 " 0.041 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 335 2.09 - 2.72: 20056 2.72 - 3.35: 33407 3.35 - 3.97: 41862 3.97 - 4.60: 65099 Nonbonded interactions: 160759 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 635 " pdb=" OE2 GLU B 836 " model vdw 1.463 2.450 nonbonded pdb=" HH TYR B 171 " pdb=" O LEU B 880 " model vdw 1.471 2.450 nonbonded pdb="HH11 ARG B 874 " pdb=" O THR B 887 " model vdw 1.484 2.450 nonbonded pdb=" O ASN A 610 " pdb=" H HIS A 778 " model vdw 1.507 2.450 nonbonded pdb=" OD2 ASP A 586 " pdb="HD21 ASN A 602 " model vdw 1.527 2.450 ... (remaining 160754 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.210 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6167 Z= 0.321 Angle : 0.989 8.496 8370 Z= 0.561 Chirality : 0.055 0.175 874 Planarity : 0.006 0.060 1101 Dihedral : 13.450 80.669 2316 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.79 % Favored : 94.80 % Rotamer: Outliers : 1.20 % Allowed : 4.19 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.20 (0.29), residues: 731 helix: -3.55 (0.43), residues: 65 sheet: 0.23 (0.36), residues: 212 loop : -0.87 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 176 HIS 0.017 0.003 HIS B 269 PHE 0.020 0.003 PHE B 90 TYR 0.025 0.006 TYR A 628 ARG 0.089 0.009 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.4986 (m-40) cc_final: 0.4719 (m-40) REVERT: B 131 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7257 (pp) REVERT: B 878 THR cc_start: 0.8570 (m) cc_final: 0.8307 (p) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.3952 time to fit residues: 55.0016 Evaluate side-chains 68 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6167 Z= 0.243 Angle : 0.700 5.579 8370 Z= 0.381 Chirality : 0.048 0.162 874 Planarity : 0.005 0.046 1101 Dihedral : 6.861 30.359 831 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.38 % Favored : 95.35 % Rotamer: Outliers : 0.15 % Allowed : 3.44 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.30), residues: 731 helix: -2.12 (0.57), residues: 54 sheet: -0.26 (0.35), residues: 201 loop : -0.45 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 618 HIS 0.007 0.002 HIS B 778 PHE 0.017 0.002 PHE B 45 TYR 0.016 0.002 TYR A 858 ARG 0.006 0.001 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.9017 (m-40) cc_final: 0.8672 (m-40) REVERT: A 854 GLU cc_start: 0.8286 (tp30) cc_final: 0.8060 (tp30) REVERT: A 870 ASN cc_start: 0.3896 (m-40) cc_final: 0.3640 (m-40) REVERT: B 852 ARG cc_start: 0.6585 (ttt-90) cc_final: 0.6249 (ptm160) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.4174 time to fit residues: 42.7317 Evaluate side-chains 51 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 59 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6167 Z= 0.204 Angle : 0.631 7.292 8370 Z= 0.341 Chirality : 0.048 0.165 874 Planarity : 0.005 0.042 1101 Dihedral : 6.358 31.535 831 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.30), residues: 731 helix: -2.10 (0.58), residues: 63 sheet: -0.56 (0.34), residues: 213 loop : -0.40 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 618 HIS 0.005 0.001 HIS A 774 PHE 0.017 0.001 PHE A 892 TYR 0.013 0.002 TYR B 239 ARG 0.003 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8397 (m110) cc_final: 0.7807 (m110) REVERT: A 693 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 602 ASN cc_start: 0.8849 (t0) cc_final: 0.8373 (t0) REVERT: B 810 TRP cc_start: 0.5653 (p-90) cc_final: 0.5336 (p-90) REVERT: B 833 LEU cc_start: 0.9095 (mm) cc_final: 0.8370 (tp) REVERT: B 852 ARG cc_start: 0.6501 (ttt-90) cc_final: 0.6210 (ptm160) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3585 time to fit residues: 30.9475 Evaluate side-chains 54 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 ASN A 876 GLN B 608 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6167 Z= 0.252 Angle : 0.633 6.127 8370 Z= 0.343 Chirality : 0.047 0.145 874 Planarity : 0.005 0.041 1101 Dihedral : 6.163 35.233 831 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.84 % Rotamer: Outliers : 0.15 % Allowed : 2.40 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.31 (0.30), residues: 731 helix: -2.32 (0.58), residues: 63 sheet: -0.97 (0.35), residues: 207 loop : -0.53 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 618 HIS 0.007 0.002 HIS B 269 PHE 0.014 0.002 PHE A 892 TYR 0.020 0.002 TYR B 13 ARG 0.004 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7942 (m-30) cc_final: 0.7602 (t0) REVERT: A 693 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 602 ASN cc_start: 0.8902 (t0) cc_final: 0.8594 (t0) REVERT: B 810 TRP cc_start: 0.5541 (p-90) cc_final: 0.5317 (p-90) REVERT: B 833 LEU cc_start: 0.9144 (mm) cc_final: 0.8467 (tp) REVERT: B 834 MET cc_start: 0.6735 (ptp) cc_final: 0.6531 (ptp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3470 time to fit residues: 33.2249 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.0270 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6167 Z= 0.196 Angle : 0.593 6.460 8370 Z= 0.320 Chirality : 0.047 0.154 874 Planarity : 0.005 0.042 1101 Dihedral : 5.934 33.965 831 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.32 (0.30), residues: 731 helix: -2.17 (0.57), residues: 69 sheet: -0.98 (0.33), residues: 222 loop : -0.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 244 HIS 0.010 0.001 HIS A 774 PHE 0.010 0.001 PHE B 45 TYR 0.011 0.001 TYR B 13 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 602 ASN cc_start: 0.8900 (t0) cc_final: 0.8594 (t0) REVERT: B 810 TRP cc_start: 0.5673 (p-90) cc_final: 0.5313 (p-90) REVERT: B 833 LEU cc_start: 0.9172 (mm) cc_final: 0.8552 (tp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3493 time to fit residues: 30.9632 Evaluate side-chains 55 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6167 Z= 0.248 Angle : 0.619 6.750 8370 Z= 0.334 Chirality : 0.047 0.144 874 Planarity : 0.005 0.042 1101 Dihedral : 5.920 33.751 831 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.31 (0.31), residues: 731 helix: -1.77 (0.69), residues: 54 sheet: -1.23 (0.33), residues: 214 loop : -0.49 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 618 HIS 0.008 0.002 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.021 0.002 TYR B 13 ARG 0.005 0.001 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 602 ASN cc_start: 0.8920 (t0) cc_final: 0.8647 (t0) REVERT: B 810 TRP cc_start: 0.5680 (p-90) cc_final: 0.5316 (p-90) REVERT: B 833 LEU cc_start: 0.9136 (mm) cc_final: 0.8624 (tp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3335 time to fit residues: 30.2060 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.1980 chunk 8 optimal weight: 0.0270 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6167 Z= 0.165 Angle : 0.585 6.959 8370 Z= 0.313 Chirality : 0.047 0.147 874 Planarity : 0.005 0.043 1101 Dihedral : 5.699 31.173 831 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 0.15 % Allowed : 0.75 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.11 (0.31), residues: 731 helix: -1.51 (0.71), residues: 48 sheet: -1.12 (0.34), residues: 209 loop : -0.39 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.008 0.001 HIS A 774 PHE 0.010 0.001 PHE A 695 TYR 0.020 0.001 TYR B 871 ARG 0.014 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8894 (t0) cc_final: 0.8682 (t0) REVERT: B 810 TRP cc_start: 0.5675 (p-90) cc_final: 0.5300 (p-90) REVERT: B 833 LEU cc_start: 0.9176 (mm) cc_final: 0.8657 (tp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.3165 time to fit residues: 28.9181 Evaluate side-chains 50 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 102 ASN B 254 ASN B 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 6167 Z= 0.310 Angle : 0.660 7.218 8370 Z= 0.358 Chirality : 0.047 0.148 874 Planarity : 0.005 0.044 1101 Dihedral : 6.094 31.243 831 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.40 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.53 (0.31), residues: 731 helix: -1.29 (0.87), residues: 41 sheet: -1.51 (0.33), residues: 213 loop : -0.70 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 176 HIS 0.008 0.002 HIS A 774 PHE 0.021 0.002 PHE A 695 TYR 0.020 0.002 TYR B 13 ARG 0.009 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 810 TRP cc_start: 0.5747 (p-90) cc_final: 0.5334 (p-90) REVERT: B 833 LEU cc_start: 0.9198 (mm) cc_final: 0.8767 (tp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3582 time to fit residues: 30.2752 Evaluate side-chains 50 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6167 Z= 0.178 Angle : 0.582 7.210 8370 Z= 0.315 Chirality : 0.047 0.147 874 Planarity : 0.005 0.043 1101 Dihedral : 5.746 28.069 831 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.07 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.44 (0.31), residues: 731 helix: -1.38 (0.75), residues: 48 sheet: -1.28 (0.33), residues: 217 loop : -0.69 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 822 HIS 0.008 0.002 HIS A 774 PHE 0.016 0.001 PHE A 695 TYR 0.018 0.002 TYR B 13 ARG 0.007 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8843 (t0) cc_final: 0.8619 (t0) REVERT: B 810 TRP cc_start: 0.5726 (p-90) cc_final: 0.5324 (p-90) REVERT: B 834 MET cc_start: 0.6786 (ptp) cc_final: 0.6355 (ptp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3467 time to fit residues: 28.4039 Evaluate side-chains 48 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6854 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6167 Z= 0.207 Angle : 0.585 7.367 8370 Z= 0.316 Chirality : 0.046 0.143 874 Planarity : 0.005 0.043 1101 Dihedral : 5.691 26.142 831 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.71 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.49 (0.31), residues: 731 helix: -1.59 (0.76), residues: 47 sheet: -1.28 (0.34), residues: 223 loop : -0.71 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 618 HIS 0.008 0.002 HIS A 774 PHE 0.014 0.001 PHE A 695 TYR 0.017 0.002 TYR B 871 ARG 0.006 0.001 ARG B 874 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8863 (t0) cc_final: 0.8609 (m-40) REVERT: B 810 TRP cc_start: 0.5750 (p-90) cc_final: 0.5329 (p-90) REVERT: B 833 LEU cc_start: 0.9149 (mm) cc_final: 0.8718 (tp) REVERT: B 834 MET cc_start: 0.6889 (ptp) cc_final: 0.6443 (ptp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3394 time to fit residues: 26.7192 Evaluate side-chains 46 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 24 optimal weight: 0.0070 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.094463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.080922 restraints weight = 104064.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.083049 restraints weight = 57012.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084500 restraints weight = 38381.721| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6167 Z= 0.161 Angle : 0.558 7.385 8370 Z= 0.301 Chirality : 0.046 0.172 874 Planarity : 0.005 0.042 1101 Dihedral : 5.453 23.156 831 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.21 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.38 (0.31), residues: 731 helix: -1.49 (0.71), residues: 53 sheet: -1.11 (0.34), residues: 224 loop : -0.67 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 601 HIS 0.007 0.002 HIS A 774 PHE 0.011 0.001 PHE A 695 TYR 0.014 0.001 TYR A 835 ARG 0.006 0.000 ARG B 874 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.27 seconds wall clock time: 59 minutes 38.79 seconds (3578.79 seconds total)