Starting phenix.real_space_refine on Mon Mar 11 09:13:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/03_2024/6a69_6987.pdb" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5045 2.51 5 N 1324 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6839 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 36, 'TRANS': 847} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 1012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1009 Unusual residues: {'NAG': 1} Classifications: {'peptide': 127, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118, None: 1} Not linked: pdbres="LYS B 246 " pdbres="NAG B 301 " Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 128, 1009 Unusual residues: {'NAG': 1} Classifications: {'peptide': 127, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118, None: 1} Not linked: pdbres="LYS B 246 " pdbres="NAG B 301 " Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1028 Time building chain proxies: 5.17, per 1000 atoms: 0.66 Number of scatterers: 7851 At special positions: 0 Unit cell: (134.193, 103.645, 128.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1443 8.00 N 1324 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 168 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 153 through 190 removed outlier: 3.994A pdb=" N ALA A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.815A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.969A pdb=" N VAL A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.945A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.733A pdb=" N CYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.086A pdb=" N VAL A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.842A pdb=" N LYS A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.973A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.857A pdb=" N LEU A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 834 through 877 removed outlier: 3.726A pdb=" N ILE A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 903 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.672A pdb=" N LEU A 912 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 925 through 949 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.667A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 4.004A pdb=" N LEU A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1025 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1058 removed outlier: 3.913A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.533A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.982A pdb=" N ILE A 472 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 707 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER A 474 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 765 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 706 " --> pdb=" O LEU A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.866A pdb=" N GLU A 683 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.650A pdb=" N MET A 585 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 616 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.471A pdb=" N LYS B 144 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 143 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.202A pdb=" N GLU B 131 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 211 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 200 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 197 " --> pdb=" O LYS B 158 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2391 1.34 - 1.46: 1487 1.46 - 1.58: 4055 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 7994 Sorted by residual: bond pdb=" C TRP A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.331 1.364 -0.032 7.90e-03 1.60e+04 1.64e+01 bond pdb=" C ALA B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.46e+01 bond pdb=" CG GLN A1020 " pdb=" CD GLN A1020 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.61e+00 bond pdb=" CB TRP A 759 " pdb=" CG TRP A 759 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.81e+00 bond pdb=" CB VAL A 792 " pdb=" CG2 VAL A 792 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 ... (remaining 7989 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.66: 165 104.66 - 112.73: 4306 112.73 - 120.80: 3934 120.80 - 128.87: 2380 128.87 - 136.94: 81 Bond angle restraints: 10866 Sorted by residual: angle pdb=" C HIS A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta sigma weight residual 121.70 134.77 -13.07 1.80e+00 3.09e-01 5.28e+01 angle pdb=" N HIS A 965 " pdb=" CA HIS A 965 " pdb=" C HIS A 965 " ideal model delta sigma weight residual 111.07 118.76 -7.69 1.07e+00 8.73e-01 5.17e+01 angle pdb=" C SER A 642 " pdb=" N GLU A 643 " pdb=" CA GLU A 643 " ideal model delta sigma weight residual 121.70 134.07 -12.37 1.80e+00 3.09e-01 4.72e+01 angle pdb=" N GLY A 228 " pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 111.42 121.78 -10.36 1.51e+00 4.39e-01 4.71e+01 angle pdb=" N PRO A 67 " pdb=" CA PRO A 67 " pdb=" CB PRO A 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 ... (remaining 10861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 4389 15.21 - 30.42: 325 30.42 - 45.64: 74 45.64 - 60.85: 11 60.85 - 76.06: 4 Dihedral angle restraints: 4803 sinusoidal: 1822 harmonic: 2981 Sorted by residual: dihedral pdb=" CA VAL A 680 " pdb=" C VAL A 680 " pdb=" N GLY A 681 " pdb=" CA GLY A 681 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N GLU A 566 " pdb=" CA GLU A 566 " ideal model delta harmonic sigma weight residual 0.00 44.37 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA PHE A 953 " pdb=" C PHE A 953 " pdb=" N PHE A 954 " pdb=" CA PHE A 954 " ideal model delta harmonic sigma weight residual -180.00 -137.23 -42.77 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1015 0.080 - 0.160: 260 0.160 - 0.240: 28 0.240 - 0.320: 4 0.320 - 0.400: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA HIS A 965 " pdb=" N HIS A 965 " pdb=" C HIS A 965 " pdb=" CB HIS A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL A 680 " pdb=" CA VAL A 680 " pdb=" CG1 VAL A 680 " pdb=" CG2 VAL A 680 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1305 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 94 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 95 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 638 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 639 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " 0.015 2.00e-02 2.50e+03 1.81e-02 8.22e+00 pdb=" CG TRP B 225 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2026 2.80 - 3.32: 7367 3.32 - 3.85: 12435 3.85 - 4.37: 13360 4.37 - 4.90: 22735 Nonbonded interactions: 57923 Sorted by model distance: nonbonded pdb=" O VAL A 515 " pdb=" OG SER A 519 " model vdw 2.275 2.440 nonbonded pdb=" O TYR A 513 " pdb=" OG1 THR A 516 " model vdw 2.308 2.440 nonbonded pdb=" O LEU A 947 " pdb=" NH1 ARG A 960 " model vdw 2.344 2.520 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 125 " model vdw 2.345 2.440 nonbonded pdb=" OE2 GLU B 135 " pdb=" NE2 GLN B 190 " model vdw 2.350 2.520 ... (remaining 57918 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.240 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.105 7994 Z= 0.689 Angle : 1.480 14.780 10866 Z= 0.816 Chirality : 0.069 0.400 1308 Planarity : 0.009 0.077 1372 Dihedral : 11.870 76.061 2872 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.53 % Favored : 86.37 % Rotamer: Outliers : 1.81 % Allowed : 4.58 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.43 % Twisted Proline : 0.00 % Twisted General : 0.91 % 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: -4.69 (0.21), residues: 1021 helix: -2.43 (0.19), residues: 449 sheet: -2.74 (0.46), residues: 103 loop : -3.93 (0.22), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP B 225 HIS 0.009 0.003 HIS A 265 PHE 0.036 0.004 PHE A 953 TYR 0.032 0.003 TYR A 445 ARG 0.008 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 217 GLN cc_start: 0.8337 (tt0) cc_final: 0.7862 (tp40) REVERT: A 235 ASP cc_start: 0.8010 (m-30) cc_final: 0.7804 (t0) REVERT: A 466 MET cc_start: 0.8832 (tmm) cc_final: 0.8292 (tmm) REVERT: A 752 GLN cc_start: 0.8888 (tt0) cc_final: 0.8684 (tm-30) REVERT: A 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8411 (mmp) REVERT: A 859 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 887 MET cc_start: 0.8963 (tpp) cc_final: 0.8445 (tpp) REVERT: A 911 LEU cc_start: 0.9705 (mt) cc_final: 0.9472 (mp) REVERT: A 1017 PHE cc_start: 0.8919 (t80) cc_final: 0.8647 (t80) REVERT: B 218 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7903 (mtp-110) outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.1837 time to fit residues: 60.0502 Evaluate side-chains 145 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 540 HIS A 711 ASN A 886 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7994 Z= 0.218 Angle : 0.807 12.822 10866 Z= 0.419 Chirality : 0.046 0.196 1308 Planarity : 0.006 0.075 1372 Dihedral : 7.077 44.398 1111 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.02 % Favored : 90.78 % Rotamer: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 1021 helix: -0.58 (0.23), residues: 462 sheet: -2.86 (0.43), residues: 106 loop : -3.58 (0.24), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 225 HIS 0.007 0.001 HIS A 971 PHE 0.024 0.001 PHE A 953 TYR 0.012 0.001 TYR B 244 ARG 0.009 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8156 (mp0) REVERT: A 122 LEU cc_start: 0.9213 (pp) cc_final: 0.8995 (tp) REVERT: A 217 GLN cc_start: 0.8257 (tt0) cc_final: 0.8020 (tp40) REVERT: A 268 GLU cc_start: 0.8347 (pp20) cc_final: 0.8066 (pp20) REVERT: A 466 MET cc_start: 0.8715 (tmm) cc_final: 0.8107 (tmm) REVERT: A 814 MET cc_start: 0.8745 (mmp) cc_final: 0.8347 (mmp) REVERT: A 887 MET cc_start: 0.8792 (tpp) cc_final: 0.8266 (tpp) REVERT: A 964 LEU cc_start: 0.8775 (tt) cc_final: 0.7898 (tt) REVERT: A 977 ASN cc_start: 0.9013 (t0) cc_final: 0.8790 (t0) REVERT: A 1006 ASN cc_start: 0.8274 (m-40) cc_final: 0.8035 (m-40) REVERT: A 1049 MET cc_start: 0.7530 (mmt) cc_final: 0.7225 (tpp) REVERT: B 157 LYS cc_start: 0.6227 (tptp) cc_final: 0.5695 (mmmt) REVERT: B 199 GLU cc_start: 0.5282 (pt0) cc_final: 0.5050 (pt0) outliers start: 2 outliers final: 2 residues processed: 214 average time/residue: 0.1617 time to fit residues: 49.3539 Evaluate side-chains 137 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7994 Z= 0.206 Angle : 0.774 12.591 10866 Z= 0.400 Chirality : 0.046 0.190 1308 Planarity : 0.006 0.083 1372 Dihedral : 6.510 42.778 1111 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.20 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.25), residues: 1021 helix: 0.22 (0.24), residues: 461 sheet: -2.62 (0.44), residues: 106 loop : -3.42 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 225 HIS 0.006 0.001 HIS A 971 PHE 0.018 0.001 PHE A 953 TYR 0.010 0.001 TYR A 445 ARG 0.003 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8079 (mp0) REVERT: A 268 GLU cc_start: 0.8123 (pp20) cc_final: 0.7915 (pp20) REVERT: A 466 MET cc_start: 0.8669 (tmm) cc_final: 0.8153 (tmm) REVERT: A 887 MET cc_start: 0.8838 (tpp) cc_final: 0.8278 (tpp) REVERT: A 928 MET cc_start: 0.7996 (tpp) cc_final: 0.7618 (tpp) REVERT: A 964 LEU cc_start: 0.8480 (tt) cc_final: 0.8176 (tt) REVERT: A 977 ASN cc_start: 0.9014 (t0) cc_final: 0.8628 (t0) REVERT: A 1049 MET cc_start: 0.7748 (mmt) cc_final: 0.7269 (mtt) REVERT: B 131 GLU cc_start: 0.6705 (tp30) cc_final: 0.6420 (tp30) REVERT: B 157 LYS cc_start: 0.6466 (tptp) cc_final: 0.6044 (mmmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1582 time to fit residues: 42.2624 Evaluate side-chains 129 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 44 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7994 Z= 0.205 Angle : 0.725 12.329 10866 Z= 0.377 Chirality : 0.045 0.187 1308 Planarity : 0.005 0.084 1372 Dihedral : 6.107 42.633 1111 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.92 % Favored : 90.88 % Rotamer: Outliers : 0.24 % Allowed : 2.77 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 1021 helix: 0.67 (0.25), residues: 457 sheet: -2.30 (0.45), residues: 114 loop : -3.39 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 759 HIS 0.007 0.001 HIS A 265 PHE 0.016 0.001 PHE A 953 TYR 0.017 0.001 TYR A 560 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8052 (mp0) REVERT: A 217 GLN cc_start: 0.7597 (tp40) cc_final: 0.7359 (mm110) REVERT: A 268 GLU cc_start: 0.8036 (pp20) cc_final: 0.7796 (pp20) REVERT: A 466 MET cc_start: 0.8710 (tmm) cc_final: 0.8383 (tmm) REVERT: A 485 MET cc_start: 0.7904 (pmm) cc_final: 0.7646 (pmm) REVERT: A 905 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 977 ASN cc_start: 0.9031 (t0) cc_final: 0.8589 (t0) REVERT: A 1049 MET cc_start: 0.7728 (mmt) cc_final: 0.7193 (mtt) REVERT: B 131 GLU cc_start: 0.6508 (tp30) cc_final: 0.6240 (tp30) outliers start: 2 outliers final: 1 residues processed: 181 average time/residue: 0.1507 time to fit residues: 39.6810 Evaluate side-chains 131 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN A 857 GLN A 859 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7994 Z= 0.189 Angle : 0.711 12.233 10866 Z= 0.371 Chirality : 0.044 0.183 1308 Planarity : 0.005 0.090 1372 Dihedral : 5.901 41.873 1111 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 0.24 % Allowed : 2.05 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.86 (0.26), residues: 1021 helix: 0.77 (0.25), residues: 459 sheet: -2.17 (0.45), residues: 114 loop : -3.27 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 153 HIS 0.003 0.001 HIS A 971 PHE 0.014 0.001 PHE A 954 TYR 0.013 0.001 TYR A 445 ARG 0.005 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8101 (mp0) REVERT: A 217 GLN cc_start: 0.7546 (tp40) cc_final: 0.7327 (mm110) REVERT: A 380 MET cc_start: 0.7956 (tpp) cc_final: 0.7702 (tpp) REVERT: A 466 MET cc_start: 0.8672 (tmm) cc_final: 0.8382 (tmm) REVERT: A 752 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8713 (pp30) REVERT: A 887 MET cc_start: 0.8543 (tpp) cc_final: 0.8124 (tpp) REVERT: A 905 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 928 MET cc_start: 0.7968 (tpp) cc_final: 0.7646 (tpp) REVERT: A 977 ASN cc_start: 0.9003 (t0) cc_final: 0.8746 (t0) REVERT: A 1020 GLN cc_start: 0.8691 (tp40) cc_final: 0.8409 (tp40) REVERT: A 1049 MET cc_start: 0.7697 (mmt) cc_final: 0.7367 (mmt) REVERT: B 157 LYS cc_start: 0.6591 (tptp) cc_final: 0.6305 (mmmt) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.1653 time to fit residues: 44.5351 Evaluate side-chains 138 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7994 Z= 0.189 Angle : 0.715 12.066 10866 Z= 0.370 Chirality : 0.044 0.181 1308 Planarity : 0.006 0.092 1372 Dihedral : 5.823 41.547 1111 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.84 % Favored : 92.06 % Rotamer: Outliers : 0.12 % Allowed : 1.69 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.69 (0.26), residues: 1021 helix: 0.94 (0.25), residues: 457 sheet: -2.02 (0.46), residues: 106 loop : -3.22 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.003 0.001 HIS A 496 PHE 0.036 0.001 PHE A 953 TYR 0.018 0.001 TYR A 560 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8014 (mp0) REVERT: A 217 GLN cc_start: 0.7505 (tp40) cc_final: 0.7031 (mm110) REVERT: A 380 MET cc_start: 0.7904 (tpp) cc_final: 0.7670 (tpp) REVERT: A 466 MET cc_start: 0.8727 (tmm) cc_final: 0.8481 (tmm) REVERT: A 905 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 928 MET cc_start: 0.7885 (tpp) cc_final: 0.7443 (tpp) REVERT: A 977 ASN cc_start: 0.9082 (t0) cc_final: 0.8757 (t0) REVERT: A 998 ASN cc_start: 0.7991 (t0) cc_final: 0.7691 (t0) REVERT: A 1006 ASN cc_start: 0.8328 (m-40) cc_final: 0.7839 (m110) REVERT: A 1049 MET cc_start: 0.7662 (mmt) cc_final: 0.7441 (mmt) REVERT: B 157 LYS cc_start: 0.6638 (tptp) cc_final: 0.6245 (mmmt) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1555 time to fit residues: 42.2186 Evaluate side-chains 142 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4432 > 50: distance: 27 - 57: 24.824 distance: 32 - 39: 7.945 distance: 33 - 62: 14.661 distance: 39 - 40: 3.808 distance: 40 - 41: 8.126 distance: 40 - 43: 4.609 distance: 41 - 42: 8.914 distance: 41 - 48: 12.214 distance: 42 - 70: 28.191 distance: 43 - 44: 8.989 distance: 44 - 45: 5.489 distance: 45 - 46: 3.660 distance: 45 - 47: 5.052 distance: 48 - 49: 14.034 distance: 49 - 50: 6.415 distance: 49 - 52: 19.445 distance: 50 - 51: 8.913 distance: 50 - 57: 16.724 distance: 51 - 78: 14.862 distance: 52 - 53: 6.690 distance: 53 - 54: 8.748 distance: 54 - 55: 10.110 distance: 54 - 56: 10.382 distance: 57 - 58: 22.831 distance: 58 - 59: 38.826 distance: 58 - 61: 16.834 distance: 59 - 60: 29.406 distance: 59 - 62: 33.916 distance: 62 - 63: 3.802 distance: 63 - 64: 13.480 distance: 63 - 66: 12.567 distance: 64 - 65: 5.613 distance: 64 - 70: 8.693 distance: 66 - 67: 11.747 distance: 66 - 68: 11.143 distance: 67 - 69: 35.089 distance: 70 - 71: 13.685 distance: 71 - 72: 9.338 distance: 71 - 74: 8.873 distance: 72 - 73: 5.106 distance: 72 - 78: 5.849 distance: 74 - 75: 10.634 distance: 75 - 76: 7.183 distance: 75 - 77: 10.141 distance: 79 - 80: 4.772 distance: 79 - 82: 7.122 distance: 80 - 81: 15.814 distance: 80 - 87: 14.396 distance: 82 - 83: 12.955 distance: 83 - 84: 17.628 distance: 84 - 85: 12.162 distance: 85 - 86: 8.152 distance: 87 - 88: 9.676 distance: 88 - 89: 20.654 distance: 88 - 91: 20.058 distance: 89 - 90: 29.670 distance: 89 - 95: 11.687 distance: 91 - 92: 5.640 distance: 91 - 93: 26.396 distance: 92 - 94: 6.301 distance: 95 - 96: 5.908 distance: 96 - 97: 31.186 distance: 96 - 99: 35.043 distance: 97 - 98: 26.166 distance: 97 - 109: 27.842 distance: 99 - 100: 20.778 distance: 100 - 101: 8.450 distance: 100 - 102: 12.575 distance: 101 - 103: 10.104 distance: 102 - 104: 4.148 distance: 104 - 106: 5.212 distance: 105 - 107: 12.156 distance: 106 - 108: 6.315 distance: 107 - 108: 6.535 distance: 109 - 110: 44.890 distance: 109 - 115: 39.502 distance: 110 - 111: 49.101 distance: 110 - 113: 41.239 distance: 111 - 112: 32.126 distance: 111 - 116: 30.211 distance: 113 - 114: 29.316 distance: 114 - 115: 12.334 distance: 116 - 117: 19.372 distance: 117 - 118: 4.103 distance: 117 - 120: 13.887 distance: 118 - 119: 14.509 distance: 118 - 121: 22.281