Starting phenix.real_space_refine on Sat Oct 12 00:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jft_36217/10_2024/8jft_36217_neut.cif" } resolution = 3.31 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= 0.011 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 15 5.16 5 C 6760 2.51 5 N 1930 2.21 5 O 2385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 11176 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8443 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "C" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 6.66, per 1000 atoms: 0.60 Number of scatterers: 11176 At special positions: 0 Unit cell: (122.72, 96.72, 117.52, 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 15 16.00 P 86 15.00 O 2385 8.00 N 1930 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 52.0% alpha, 10.3% beta 19 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.741A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.683A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.188A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 444' Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 483 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 removed outlier: 3.764A pdb=" N LEU A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 705 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.920A pdb=" N TYR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 31 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 772 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 33 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA4, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 805 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 892 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA A 964 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 918 " --> pdb=" O PHE A 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 962 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 936 Processing sheet with id=AA9, first strand: chain 'A' and resid 1017 through 1019 removed outlier: 7.507A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 81 448 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1696 1.31 - 1.43: 3472 1.43 - 1.56: 6190 1.56 - 1.68: 170 1.68 - 1.81: 27 Bond restraints: 11555 Sorted by residual: bond pdb=" C ARG A 47 " pdb=" O ARG A 47 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.29e+01 bond pdb=" CA SER A 49 " pdb=" CB SER A 49 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.59e-02 3.96e+03 2.07e+01 bond pdb=" CA SER A 106 " pdb=" CB SER A 106 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.62e+01 bond pdb=" CA SER C 76 " pdb=" CB SER C 76 " ideal model delta sigma weight residual 1.532 1.459 0.072 1.82e-02 3.02e+03 1.58e+01 ... (remaining 11550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 14134 2.03 - 4.05: 1629 4.05 - 6.08: 198 6.08 - 8.10: 29 8.10 - 10.13: 5 Bond angle restraints: 15995 Sorted by residual: angle pdb=" N ARG A 51 " pdb=" CA ARG A 51 " pdb=" C ARG A 51 " ideal model delta sigma weight residual 111.28 102.89 8.39 1.09e+00 8.42e-01 5.92e+01 angle pdb=" N LEU A 110 " pdb=" CA LEU A 110 " pdb=" C LEU A 110 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.13e+01 angle pdb=" N GLU A 45 " pdb=" CA GLU A 45 " pdb=" C GLU A 45 " ideal model delta sigma weight residual 111.82 103.58 8.24 1.16e+00 7.43e-01 5.05e+01 angle pdb=" N PRO A1014 " pdb=" CA PRO A1014 " pdb=" C PRO A1014 " ideal model delta sigma weight residual 114.03 122.59 -8.56 1.23e+00 6.61e-01 4.84e+01 angle pdb=" N TYR C 147 " pdb=" CA TYR C 147 " pdb=" C TYR C 147 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 ... (remaining 15990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6780 35.58 - 71.16: 315 71.16 - 106.73: 30 106.73 - 142.31: 2 142.31 - 177.89: 2 Dihedral angle restraints: 7129 sinusoidal: 3701 harmonic: 3428 Sorted by residual: dihedral pdb=" C4' U B 73 " pdb=" C3' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.95 -68.95 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" O4' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " pdb=" C3' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 31.37 -66.37 1 8.00e+00 1.56e-02 8.99e+01 dihedral pdb=" O4' U B 11 " pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sinusoidal sigma weight residual -128.00 49.89 -177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1229 0.070 - 0.140: 350 0.140 - 0.211: 196 0.211 - 0.281: 51 0.281 - 0.351: 11 Chirality restraints: 1837 Sorted by residual: chirality pdb=" CA PRO A1014 " pdb=" N PRO A1014 " pdb=" C PRO A1014 " pdb=" CB PRO A1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA TYR C 77 " pdb=" N TYR C 77 " pdb=" C TYR C 77 " pdb=" CB TYR C 77 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 880 " pdb=" N ILE A 880 " pdb=" C ILE A 880 " pdb=" CB ILE A 880 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1834 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 973 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS A 973 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS A 973 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 974 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1006 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU A1006 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU A1006 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A1007 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1020 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ILE A1020 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE A1020 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA A1021 " -0.019 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2683 2.79 - 3.32: 10879 3.32 - 3.85: 18832 3.85 - 4.37: 22503 4.37 - 4.90: 34978 Nonbonded interactions: 89875 Sorted by model distance: nonbonded pdb=" O ARG A 209 " pdb=" O2' U B 16 " model vdw 2.264 3.040 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP A 545 " pdb=" OH TYR A 553 " model vdw 2.287 3.040 nonbonded pdb=" O2' G B 87 " pdb=" OP1 U B 88 " model vdw 2.297 3.040 nonbonded pdb=" ND2 ASN A 413 " pdb=" N GLN A 414 " model vdw 2.298 3.200 ... (remaining 89870 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.008 0.073 11555 Z= 0.536 Angle : 1.270 10.126 15995 Z= 0.943 Chirality : 0.089 0.351 1837 Planarity : 0.005 0.041 1740 Dihedral : 18.180 177.886 4923 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 5.48 % Favored : 93.62 % Cbeta Deviations : 0.18 % 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: -0.00 (0.24), residues: 1145 helix: 0.78 (0.23), residues: 527 sheet: 0.09 (0.51), residues: 101 loop : -0.78 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.006 0.001 HIS A 773 PHE 0.019 0.002 PHE C 165 TYR 0.026 0.002 TYR A 256 ARG 0.008 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8177 (p90) cc_final: 0.7961 (p90) REVERT: A 232 MET cc_start: 0.8264 (mmt) cc_final: 0.7096 (ttt) REVERT: A 243 GLU cc_start: 0.7998 (tp30) cc_final: 0.7785 (tp30) REVERT: A 331 ASP cc_start: 0.8019 (m-30) cc_final: 0.7797 (m-30) REVERT: A 366 GLU cc_start: 0.8507 (tt0) cc_final: 0.8217 (tt0) REVERT: A 386 LEU cc_start: 0.8671 (mt) cc_final: 0.8233 (mt) REVERT: A 440 LEU cc_start: 0.8906 (mm) cc_final: 0.8393 (mm) REVERT: A 534 CYS cc_start: 0.7587 (t) cc_final: 0.6827 (t) REVERT: A 605 LYS cc_start: 0.9398 (tmtt) cc_final: 0.9179 (tptt) REVERT: A 696 LYS cc_start: 0.8625 (mmtm) cc_final: 0.7926 (pttt) REVERT: A 769 TYR cc_start: 0.8358 (m-80) cc_final: 0.7915 (m-80) REVERT: A 813 ASN cc_start: 0.8398 (t0) cc_final: 0.7839 (t0) REVERT: A 833 ASP cc_start: 0.7947 (t70) cc_final: 0.7053 (t70) REVERT: A 987 ASP cc_start: 0.8219 (p0) cc_final: 0.7818 (p0) REVERT: A 996 MET cc_start: 0.7650 (mtm) cc_final: 0.6912 (mtm) REVERT: A 1024 THR cc_start: 0.9254 (m) cc_final: 0.8983 (p) REVERT: C 78 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (mt) REVERT: C 93 ASP cc_start: 0.8801 (t0) cc_final: 0.8519 (t0) REVERT: C 95 TYR cc_start: 0.7786 (m-80) cc_final: 0.7432 (m-80) REVERT: C 106 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 129 ASN cc_start: 0.7823 (t0) cc_final: 0.7173 (t0) outliers start: 9 outliers final: 2 residues processed: 221 average time/residue: 0.2368 time to fit residues: 75.4267 Evaluate side-chains 155 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 120 ASN A 137 GLN A 141 ASN A 154 GLN A 252 ASN A 264 ASN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 413 ASN A 414 GLN A 570 ASN A 580 ASN A 695 ASN A 785 ASN A 863 ASN A 968 ASN A 990 ASN C 163 HIS C 169 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11555 Z= 0.438 Angle : 0.724 11.612 15995 Z= 0.372 Chirality : 0.044 0.156 1837 Planarity : 0.004 0.036 1740 Dihedral : 18.803 177.947 2582 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 10.77 % Favored : 86.34 % 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: -0.00 (0.24), residues: 1145 helix: 0.90 (0.22), residues: 544 sheet: -0.47 (0.45), residues: 124 loop : -0.86 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 408 HIS 0.012 0.002 HIS A 330 PHE 0.020 0.002 PHE A 925 TYR 0.018 0.002 TYR A 789 ARG 0.006 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.211 Fit side-chains REVERT: A 35 LEU cc_start: 0.8530 (mp) cc_final: 0.8295 (mp) REVERT: A 76 LEU cc_start: 0.7979 (mt) cc_final: 0.7744 (mp) REVERT: A 232 MET cc_start: 0.8359 (mmt) cc_final: 0.7397 (ttp) REVERT: A 362 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 366 GLU cc_start: 0.8303 (tt0) cc_final: 0.7959 (tt0) REVERT: A 386 LEU cc_start: 0.8696 (mt) cc_final: 0.8213 (mt) REVERT: A 406 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 478 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 534 CYS cc_start: 0.7463 (t) cc_final: 0.7033 (t) REVERT: A 605 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9112 (tptt) REVERT: A 657 MET cc_start: 0.8107 (mmm) cc_final: 0.7834 (mmt) REVERT: A 677 ASN cc_start: 0.8298 (t0) cc_final: 0.7828 (t0) REVERT: A 696 LYS cc_start: 0.8403 (mmtm) cc_final: 0.7781 (pttp) REVERT: A 833 ASP cc_start: 0.7925 (t70) cc_final: 0.6997 (t70) REVERT: A 1024 THR cc_start: 0.9287 (m) cc_final: 0.8899 (p) REVERT: C 93 ASP cc_start: 0.8791 (t0) cc_final: 0.8532 (t0) REVERT: C 95 TYR cc_start: 0.7984 (m-80) cc_final: 0.7576 (m-80) REVERT: C 97 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8106 (t80) outliers start: 29 outliers final: 15 residues processed: 162 average time/residue: 0.2307 time to fit residues: 54.0812 Evaluate side-chains 149 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 0.3980 chunk 99 optimal weight: 0.0770 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11555 Z= 0.213 Angle : 0.548 7.399 15995 Z= 0.289 Chirality : 0.039 0.133 1837 Planarity : 0.003 0.032 1740 Dihedral : 18.603 177.841 2579 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.29 % Allowed : 12.76 % Favored : 84.95 % 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: 0.34 (0.25), residues: 1145 helix: 1.28 (0.22), residues: 546 sheet: -0.47 (0.46), residues: 119 loop : -0.79 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 408 HIS 0.007 0.001 HIS A 330 PHE 0.016 0.002 PHE A 914 TYR 0.032 0.001 TYR A 18 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 TYR cc_start: 0.8566 (t80) cc_final: 0.8320 (t80) REVERT: A 362 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 366 GLU cc_start: 0.8300 (tt0) cc_final: 0.7920 (mm-30) REVERT: A 386 LEU cc_start: 0.8672 (mt) cc_final: 0.8220 (mt) REVERT: A 394 ASN cc_start: 0.7631 (t0) cc_final: 0.7409 (t0) REVERT: A 406 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7014 (tp30) REVERT: A 440 LEU cc_start: 0.9041 (mm) cc_final: 0.8751 (mm) REVERT: A 478 LEU cc_start: 0.8481 (tp) cc_final: 0.8163 (tt) REVERT: A 534 CYS cc_start: 0.7357 (t) cc_final: 0.6923 (t) REVERT: A 605 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9112 (tptt) REVERT: A 677 ASN cc_start: 0.8108 (t0) cc_final: 0.6919 (m-40) REVERT: A 696 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7781 (pttp) REVERT: A 813 ASN cc_start: 0.8714 (t0) cc_final: 0.8164 (t0) REVERT: A 829 MET cc_start: 0.8634 (mtp) cc_final: 0.7835 (mtp) REVERT: A 833 ASP cc_start: 0.7800 (t70) cc_final: 0.6281 (p0) REVERT: A 910 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8452 (mmtm) REVERT: A 987 ASP cc_start: 0.8276 (p0) cc_final: 0.7860 (p0) REVERT: A 1024 THR cc_start: 0.9262 (m) cc_final: 0.8935 (p) REVERT: C 93 ASP cc_start: 0.8738 (t0) cc_final: 0.8513 (t0) REVERT: C 95 TYR cc_start: 0.7899 (m-80) cc_final: 0.7405 (m-80) REVERT: C 97 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8072 (t80) outliers start: 23 outliers final: 12 residues processed: 172 average time/residue: 0.2347 time to fit residues: 58.0416 Evaluate side-chains 155 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: