Starting phenix.real_space_refine (version: 1.20rc4) on Thu Dec 2 00:04:35 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5c_21541/12_2021/6w5c_21541.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 10183 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 35, 'TRANS': 987} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "C" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 740 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1055 Classifications: {'RNA': 50} Modifications used: {'rna3p_pyr': 21, 'rna2p_pur': 3, 'rna3p_pur': 17, 'rna2p_pyr': 9} Link IDs: {'rna3p': 37, 'rna2p': 12} Time building chain proxies: 6.37, per 1000 atoms: 0.63 Number of scatterers: 10183 At special positions: 0 Unit cell: (90.61, 134.316, 101.27, 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 36 16.00 P 105 15.00 O 2162 8.00 N 1769 7.00 C 6111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 1.6 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 56.4% alpha, 6.9% beta 36 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.692A pdb=" N LEU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.194A pdb=" N ASN A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 297 through 333 removed outlier: 3.520A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 347 through 350 removed outlier: 3.792A pdb=" N SER A 350 " --> pdb=" O PHE A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.771A pdb=" N GLY A 369 " --> pdb=" O HIS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.668A pdb=" N SER A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 422 removed outlier: 3.798A pdb=" N LYS A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 491 through 501 removed outlier: 3.663A pdb=" N LEU A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.577A pdb=" N LEU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.644A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 722 " --> pdb=" O PHE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.527A pdb=" N ALA A 775 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 800 through 822 removed outlier: 3.781A pdb=" N PHE A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.794A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.557A pdb=" N LEU A 971 " --> pdb=" O PRO A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.507A pdb=" N ARG A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 4.333A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.997A pdb=" N ASN A 477 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY A 486 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 479 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 488 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 523 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 530 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.586A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.270A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 680 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 894 " --> pdb=" O TYR A 646 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 937 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 891 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 939 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 893 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 688 removed outlier: 3.541A pdb=" N TYR A 695 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.604A pdb=" N THR A1059 " --> pdb=" O VAL A1070 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2562 1.33 - 1.45: 2443 1.45 - 1.57: 5330 1.57 - 1.69: 206 1.69 - 1.81: 60 Bond restraints: 10601 Sorted by residual: bond pdb=" N TYR A 754 " pdb=" CA TYR A 754 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.33e-02 5.65e+03 1.11e+01 bond pdb=" N ASP A 788 " pdb=" CA ASP A 788 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.24e-02 6.50e+03 1.09e+01 bond pdb=" N GLY A 789 " pdb=" CA GLY A 789 " ideal model delta sigma weight residual 1.449 1.481 -0.032 1.23e-02 6.61e+03 6.92e+00 bond pdb=" N SER A 167 " pdb=" CA SER A 167 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N LYS A 790 " pdb=" CA LYS A 790 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.70e+00 ... (remaining 10596 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.29: 770 106.29 - 113.26: 5778 113.26 - 120.23: 4017 120.23 - 127.19: 3940 127.19 - 134.16: 269 Bond angle restraints: 14774 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.36 110.43 -7.07 8.80e-01 1.29e+00 6.45e+01 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" CB PRO A 955 " ideal model delta sigma weight residual 103.25 110.33 -7.08 1.05e+00 9.07e-01 4.55e+01 angle pdb=" N ASN A1064 " pdb=" CA ASN A1064 " pdb=" C ASN A1064 " ideal model delta sigma weight residual 111.07 105.24 5.83 1.07e+00 8.73e-01 2.97e+01 angle pdb=" C VAL A1061 " pdb=" N ASN A1062 " pdb=" CA ASN A1062 " ideal model delta sigma weight residual 122.77 129.88 -7.11 1.33e+00 5.65e-01 2.86e+01 angle pdb=" N ASP A 788 " pdb=" CA ASP A 788 " pdb=" C ASP A 788 " ideal model delta sigma weight residual 111.40 117.85 -6.45 1.22e+00 6.72e-01 2.79e+01 ... (remaining 14769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 5874 35.31 - 70.62: 209 70.62 - 105.93: 9 105.93 - 141.24: 0 141.24 - 176.55: 4 Dihedral angle restraints: 6096 sinusoidal: 3087 harmonic: 3009 Sorted by residual: dihedral pdb=" O4' U B -19 " pdb=" C1' U B -19 " pdb=" N1 U B -19 " pdb=" C2 U B -19 " ideal model delta sinusoidal sigma weight residual 232.00 55.45 176.55 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual -128.00 38.49 -166.49 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U B -21 " pdb=" C1' U B -21 " pdb=" N1 U B -21 " pdb=" C2 U B -21 " ideal model delta sinusoidal sigma weight residual -128.00 36.38 -164.38 1 1.70e+01 3.46e-03 6.52e+01 ... (remaining 6093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1342 0.044 - 0.088: 250 0.088 - 0.132: 76 0.132 - 0.176: 5 0.176 - 0.220: 4 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA PRO A 955 " pdb=" N PRO A 955 " pdb=" C PRO A 955 " pdb=" CB PRO A 955 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 347 " pdb=" N PHE A 347 " pdb=" C PHE A 347 " pdb=" CB PHE A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 1674 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 693 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS A 693 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS A 693 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 694 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 754 " -0.042 2.00e-02 2.50e+03 2.33e-02 1.09e+01 pdb=" CG TYR A 754 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 754 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 754 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 754 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 754 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 754 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 754 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 787 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ARG A 787 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG A 787 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 788 " 0.019 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 297 2.66 - 3.22: 9836 3.22 - 3.78: 17541 3.78 - 4.34: 24337 4.34 - 4.90: 37584 Nonbonded interactions: 89595 Sorted by model distance: nonbonded pdb=" OE1 GLN A 186 " pdb=" OG1 THR A 187 " model vdw 2.103 2.440 nonbonded pdb=" O TYR A 104 " pdb=" OG SER A 105 " model vdw 2.134 2.440 nonbonded pdb=" OH TYR A 542 " pdb=" OE1 GLU A 596 " model vdw 2.202 2.440 nonbonded pdb=" OD2 ASP A 647 " pdb=" ND2 ASN A 649 " model vdw 2.206 2.520 nonbonded pdb=" NE ARG A 715 " pdb=" OE2 GLU A 781 " model vdw 2.215 2.520 ... (remaining 89590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 105 5.49 5 S 36 5.16 5 C 6111 2.51 5 N 1769 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.510 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 34.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:10.460 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 10601 Z= 0.240 Angle : 0.637 8.640 14774 Z= 0.405 Chirality : 0.039 0.220 1677 Planarity : 0.003 0.039 1508 Dihedral : 16.122 176.553 4150 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.43 % Favored : 92.37 % Rotamer Outliers : 0.85 % 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: -1.44 (0.26), residues: 1009 helix: 0.66 (0.23), residues: 550 sheet: -2.34 (0.52), residues: 99 loop : -3.16 (0.27), residues: 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 1.0724 time to fit residues: 124.7767 Evaluate side-chains 68 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0879 time to fit residues: 1.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10601 Z= 0.215 Angle : 0.571 10.198 14774 Z= 0.307 Chirality : 0.038 0.152 1677 Planarity : 0.003 0.034 1508 Dihedral : 17.965 178.125 2241 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 1009 helix: 1.16 (0.23), residues: 549 sheet: -2.05 (0.52), residues: 99 loop : -2.79 (0.28), residues: 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.069 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 90 average time/residue: 0.9609 time to fit residues: 95.6901 Evaluate side-chains 72 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2281 time to fit residues: 2.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.0570 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10601 Z= 0.280 Angle : 0.566 8.496 14774 Z= 0.304 Chirality : 0.039 0.149 1677 Planarity : 0.003 0.036 1508 Dihedral : 17.796 179.204 2241 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 3.27 % 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: -0.70 (0.27), residues: 1009 helix: 1.15 (0.22), residues: 552 sheet: -1.83 (0.51), residues: 101 loop : -2.72 (0.29), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 1.078 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.9799 time to fit residues: 104.6009 Evaluate side-chains 88 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.1848 time to fit residues: 2.5186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 654 ASN A 942 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 10601 Z= 0.263 Angle : 0.551 8.734 14774 Z= 0.297 Chirality : 0.038 0.147 1677 Planarity : 0.003 0.033 1508 Dihedral : 17.752 179.057 2241 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 2.91 % 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: -0.52 (0.27), residues: 1009 helix: 1.26 (0.22), residues: 552 sheet: -1.57 (0.51), residues: 101 loop : -2.65 (0.29), residues: 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.057 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 96 average time/residue: 0.9879 time to fit residues: 104.6211 Evaluate side-chains 89 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3253 time to fit residues: 3.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10601 Z= 0.210 Angle : 0.528 8.906 14774 Z= 0.285 Chirality : 0.036 0.143 1677 Planarity : 0.003 0.034 1508 Dihedral : 17.625 179.705 2241 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 2.42 % 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: -0.40 (0.27), residues: 1009 helix: 1.30 (0.22), residues: 554 sheet: -1.40 (0.55), residues: 89 loop : -2.52 (0.29), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.038 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 1.0127 time to fit residues: 104.3931 Evaluate side-chains 80 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1501 time to fit residues: 1.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 0.0010 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 190 GLN A 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10601 Z= 0.188 Angle : 0.515 8.731 14774 Z= 0.277 Chirality : 0.036 0.154 1677 Planarity : 0.003 0.033 1508 Dihedral : 17.520 179.807 2241 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 1009 helix: 1.46 (0.22), residues: 553 sheet: -1.20 (0.55), residues: 89 loop : -2.48 (0.29), residues: 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.130 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.9846 time to fit residues: 99.7462 Evaluate side-chains 82 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.1778 time to fit residues: 2.1409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 10601 Z= 0.285 Angle : 0.556 10.130 14774 Z= 0.297 Chirality : 0.038 0.147 1677 Planarity : 0.004 0.040 1508 Dihedral : 17.616 178.666 2241 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 2.79 % 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: -0.26 (0.27), residues: 1009 helix: 1.39 (0.22), residues: 553 sheet: -1.24 (0.52), residues: 97 loop : -2.45 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.938 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.9807 time to fit residues: 101.4718 Evaluate side-chains 84 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.6254 time to fit residues: 2.7541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 10601 Z= 0.382 Angle : 0.596 6.854 14774 Z= 0.320 Chirality : 0.041 0.150 1677 Planarity : 0.004 0.035 1508 Dihedral : 17.817 177.285 2241 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 1009 helix: 1.13 (0.22), residues: 557 sheet: -1.51 (0.51), residues: 99 loop : -2.35 (0.31), residues: 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 1.036 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 1.0843 time to fit residues: 111.1828 Evaluate side-chains 91 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.2610 time to fit residues: 2.9485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 94 optimal weight: 50.0000 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 10601 Z= 0.250 Angle : 0.566 12.482 14774 Z= 0.302 Chirality : 0.038 0.159 1677 Planarity : 0.003 0.034 1508 Dihedral : 17.711 179.091 2241 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 2.18 % 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: -0.39 (0.27), residues: 1009 helix: 1.19 (0.22), residues: 558 sheet: -1.32 (0.51), residues: 97 loop : -2.37 (0.30), residues: 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.9623 time to fit residues: 98.8770 Evaluate side-chains 87 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1935 time to fit residues: 1.8969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 101 optimal weight: 0.0980 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 10601 Z= 0.176 Angle : 0.517 10.394 14774 Z= 0.279 Chirality : 0.035 0.151 1677 Planarity : 0.003 0.033 1508 Dihedral : 17.411 177.984 2241 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 1.82 % 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: -0.13 (0.27), residues: 1009 helix: 1.47 (0.22), residues: 559 sheet: -1.07 (0.52), residues: 97 loop : -2.44 (0.30), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.067 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.9254 time to fit residues: 100.2791 Evaluate side-chains 82 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.3506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 654 ASN A1062 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095282 restraints weight = 16865.701| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.28 r_work: 0.3385 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.3356 rms_B_bonded: 2.13 restraints_weight: 0.1250 r_work: 0.3342 rms_B_bonded: 2.23 restraints_weight: 0.0625 r_work: 0.3327 rms_B_bonded: 2.36 restraints_weight: 0.0312 r_work: 0.3311 rms_B_bonded: 2.52 restraints_weight: 0.0156 r_work: 0.3295 rms_B_bonded: 2.71 restraints_weight: 0.0078 r_work: 0.3278 rms_B_bonded: 2.94 restraints_weight: 0.0039 r_work: 0.3259 rms_B_bonded: 3.20 restraints_weight: 0.0020 r_work: 0.3239 rms_B_bonded: 3.50 restraints_weight: 0.0010 r_work: 0.3218 rms_B_bonded: 3.83 restraints_weight: 0.0005 r_work: 0.3195 rms_B_bonded: 4.21 restraints_weight: 0.0002 r_work: 0.3171 rms_B_bonded: 4.64 restraints_weight: 0.0001 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 10601 Z= 0.209 Angle : 0.540 8.769 14774 Z= 0.287 Chirality : 0.037 0.152 1677 Planarity : 0.003 0.033 1508 Dihedral : 17.459 179.878 2241 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 1.94 % 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: -0.10 (0.27), residues: 1009 helix: 1.46 (0.22), residues: 559 sheet: -0.99 (0.52), residues: 97 loop : -2.39 (0.30), residues: 353 =============================================================================== Job complete usr+sys time: 2401.33 seconds wall clock time: 45 minutes 0.09 seconds (2700.09 seconds total)