Starting phenix.real_space_refine on Thu Mar 6 01:33:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxe_37904/03_2025/8wxe_37904.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 2865 2.51 5 N 692 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4388 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 853 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "f" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "g" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 2 Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.14, per 1000 atoms: 0.72 Number of scatterers: 4388 At special positions: 0 Unit cell: (94.569, 82.612, 98.917, 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 37 16.00 O 794 8.00 N 692 7.00 C 2865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 534.5 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 42.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'a' and resid 27 through 54 removed outlier: 4.323A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 54 Processing helix chain 'd' and resid 100 through 125 removed outlier: 3.787A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR d 110 " --> pdb=" O GLY d 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.706A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE e 135 " --> pdb=" O ALA e 131 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 153 Processing helix chain 'g' and resid 111 through 140 removed outlier: 4.749A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 258 through 288 removed outlier: 3.667A pdb=" N PHE m 288 " --> pdb=" O THR m 284 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 288 removed outlier: 3.891A pdb=" N TYR n 264 " --> pdb=" O THR n 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET n 265 " --> pdb=" O SER n 261 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL n 275 " --> pdb=" O LEU n 271 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR n 276 " --> pdb=" O LYS n 272 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 33 through 36 removed outlier: 7.108A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 3.668A pdb=" N VAL d 44 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY d 69 " --> pdb=" O VAL d 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL d 88 " --> pdb=" O GLY d 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 4.132A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 47 removed outlier: 3.536A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123 removed outlier: 3.588A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 4.439A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 55 through 57 removed outlier: 7.219A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 84 through 85 removed outlier: 4.063A pdb=" N TYR g 85 " --> pdb=" O LEU g 97 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 215 hydrogen bonds defined for protein. 624 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: 1.04 Time building geometry restraints manager: 1.42 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: 1333 1.34 - 1.47: 1083 1.47 - 1.59: 2000 1.59 - 1.71: 1 1.71 - 1.83: 51 Bond restraints: 4468 Sorted by residual: bond pdb=" CB PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.72e+00 bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" N PRO g 96 " pdb=" CA PRO g 96 " ideal model delta sigma weight residual 1.469 1.450 0.018 1.28e-02 6.10e+03 2.05e+00 bond pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" C3 CLR g 201 " pdb=" O1 CLR g 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 5950 2.74 - 5.48: 76 5.48 - 8.22: 17 8.22 - 10.96: 6 10.96 - 13.70: 2 Bond angle restraints: 6051 Sorted by residual: angle pdb=" CA PRO g 96 " pdb=" N PRO g 96 " pdb=" CD PRO g 96 " ideal model delta sigma weight residual 112.00 98.30 13.70 1.40e+00 5.10e-01 9.58e+01 angle pdb=" CA GLU f 106 " pdb=" CB GLU f 106 " pdb=" CG GLU f 106 " ideal model delta sigma weight residual 114.10 123.42 -9.32 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CB MET f 123 " pdb=" CG MET f 123 " pdb=" SD MET f 123 " ideal model delta sigma weight residual 112.70 124.29 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N PRO g 96 " pdb=" CD PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 103.20 97.67 5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" CB PRO g 96 " ideal model delta sigma weight residual 103.25 99.87 3.38 1.05e+00 9.07e-01 1.04e+01 ... (remaining 6046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2228 17.86 - 35.72: 372 35.72 - 53.58: 94 53.58 - 71.44: 20 71.44 - 89.30: 4 Dihedral angle restraints: 2718 sinusoidal: 1122 harmonic: 1596 Sorted by residual: dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual -86.00 -158.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -147.58 61.58 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 2715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 472 0.034 - 0.068: 170 0.068 - 0.102: 53 0.102 - 0.136: 21 0.136 - 0.170: 5 Chirality restraints: 721 Sorted by residual: chirality pdb=" CA PRO f 105 " pdb=" N PRO f 105 " pdb=" C PRO f 105 " pdb=" CB PRO f 105 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C20 CLR g 201 " pdb=" C17 CLR g 201 " pdb=" C21 CLR g 201 " pdb=" C22 CLR g 201 " both_signs ideal model delta sigma weight residual False 2.59 2.43 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN g 28 " pdb=" N ASN g 28 " pdb=" C ASN g 28 " pdb=" CB ASN g 28 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 718 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " 0.119 5.00e-02 4.00e+02 1.68e-01 4.53e+01 pdb=" N PRO g 96 " -0.290 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE d 24 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO d 25 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO d 25 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO d 25 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU f 86 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" CD GLU f 86 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU f 86 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU f 86 " -0.013 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 223 2.72 - 3.27: 4463 3.27 - 3.81: 7031 3.81 - 4.36: 7314 4.36 - 4.90: 12724 Nonbonded interactions: 31755 Sorted by model distance: nonbonded pdb=" O SER f 41 " pdb=" OG1 THR f 44 " model vdw 2.178 3.040 nonbonded pdb=" NZ LYS f 104 " pdb=" OE1 GLU f 106 " model vdw 2.199 3.120 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.216 3.040 nonbonded pdb=" N GLU e 124 " pdb=" OE1 GLU e 124 " model vdw 2.272 3.120 nonbonded pdb=" OG SER g 125 " pdb=" NZ LYS n 272 " model vdw 2.321 3.120 ... (remaining 31750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 49 or resid 58 through 65 or resid 75 through 1 \ 53)) selection = (chain 'f' and (resid 33 through 65 or resid 75 through 101 or resid 109 through \ 153)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.930 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 0.130 4468 Z= 0.244 Angle : 0.862 13.704 6051 Z= 0.451 Chirality : 0.043 0.170 721 Planarity : 0.008 0.168 728 Dihedral : 18.180 89.302 1663 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.04 % Allowed : 40.73 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.35), residues: 520 helix: 1.55 (0.33), residues: 217 sheet: -1.07 (0.61), residues: 71 loop : -2.43 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 59 HIS 0.005 0.001 HIS g 29 PHE 0.009 0.001 PHE f 110 TYR 0.023 0.001 TYR f 36 ARG 0.007 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 52 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6177 (ttt180) REVERT: d 63 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8450 (mtp85) REVERT: d 92 MET cc_start: 0.8431 (mtp) cc_final: 0.7769 (mmt) REVERT: d 97 VAL cc_start: 0.8955 (t) cc_final: 0.8619 (p) REVERT: d 109 VAL cc_start: 0.8934 (m) cc_final: 0.8674 (p) REVERT: e 92 GLN cc_start: 0.8518 (tt0) cc_final: 0.8028 (tt0) REVERT: e 95 TYR cc_start: 0.6958 (m-80) cc_final: 0.6366 (m-10) REVERT: e 145 LEU cc_start: 0.8539 (mm) cc_final: 0.8173 (tt) REVERT: e 147 LEU cc_start: 0.8127 (tt) cc_final: 0.7907 (mm) REVERT: f 97 VAL cc_start: 0.8610 (m) cc_final: 0.8233 (p) REVERT: f 101 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7068 (mpt180) REVERT: f 121 ASN cc_start: 0.9297 (t0) cc_final: 0.8889 (t0) REVERT: f 125 MET cc_start: 0.7019 (pmm) cc_final: 0.6524 (pmm) REVERT: g 34 TYR cc_start: 0.8520 (t80) cc_final: 0.8285 (t80) REVERT: g 39 ASP cc_start: 0.7355 (m-30) cc_final: 0.6303 (m-30) REVERT: g 73 ASN cc_start: 0.9503 (t0) cc_final: 0.9215 (t0) REVERT: g 103 MET cc_start: 0.7179 (mmp) cc_final: 0.6798 (mmp) REVERT: g 119 LEU cc_start: 0.9204 (tp) cc_final: 0.8856 (tp) REVERT: n 259 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7496 (t0) outliers start: 10 outliers final: 5 residues processed: 221 average time/residue: 0.1516 time to fit residues: 41.8368 Evaluate side-chains 164 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain n residue 259 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 89 HIS e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.104569 restraints weight = 10093.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107755 restraints weight = 6866.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108517 restraints weight = 4556.835| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4468 Z= 0.360 Angle : 0.834 8.261 6051 Z= 0.424 Chirality : 0.046 0.159 721 Planarity : 0.005 0.083 728 Dihedral : 7.864 58.159 662 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 9.78 % Allowed : 33.40 % Favored : 56.82 % 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: -0.57 (0.35), residues: 520 helix: 1.83 (0.32), residues: 224 sheet: -1.21 (0.57), residues: 77 loop : -2.55 (0.34), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 72 HIS 0.004 0.001 HIS g 29 PHE 0.022 0.002 PHE g 127 TYR 0.026 0.002 TYR f 149 ARG 0.005 0.001 ARG g 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 30 LYS cc_start: 0.8468 (tmmt) cc_final: 0.7954 (mmtm) REVERT: a 46 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (tt) REVERT: a 52 ARG cc_start: 0.6552 (ttt180) cc_final: 0.6170 (ttt180) REVERT: b 34 LEU cc_start: 0.7987 (tt) cc_final: 0.7293 (mm) REVERT: d 63 ARG cc_start: 0.8981 (ttm170) cc_final: 0.8254 (mtp-110) REVERT: d 72 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7313 (tpt-90) REVERT: d 92 MET cc_start: 0.8136 (mtp) cc_final: 0.7607 (mmt) REVERT: d 97 VAL cc_start: 0.8827 (t) cc_final: 0.8607 (p) REVERT: d 98 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7372 (tm-30) REVERT: d 120 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8462 (tp) REVERT: e 92 GLN cc_start: 0.8632 (tt0) cc_final: 0.8287 (tt0) REVERT: e 145 LEU cc_start: 0.8620 (mm) cc_final: 0.8078 (tt) REVERT: e 147 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8024 (mm) REVERT: f 121 ASN cc_start: 0.9215 (t0) cc_final: 0.8740 (t0) REVERT: f 125 MET cc_start: 0.7289 (pmm) cc_final: 0.7072 (pmm) REVERT: g 34 TYR cc_start: 0.8774 (t80) cc_final: 0.8465 (t80) REVERT: g 38 GLU cc_start: 0.8101 (pm20) cc_final: 0.7541 (pm20) REVERT: g 73 ASN cc_start: 0.9475 (t0) cc_final: 0.9239 (t0) REVERT: g 82 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8480 (mmt-90) REVERT: g 111 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8619 (p0) REVERT: g 119 LEU cc_start: 0.9104 (tp) cc_final: 0.8806 (tp) REVERT: m 261 MET cc_start: 0.8539 (mmm) cc_final: 0.8297 (tpp) REVERT: n 259 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7233 (t0) outliers start: 48 outliers final: 28 residues processed: 196 average time/residue: 0.1416 time to fit residues: 35.0558 Evaluate side-chains 189 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 56 PHE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2993 > 50: distance: 22 - 27: 31.060 distance: 27 - 28: 19.547 distance: 28 - 29: 20.276 distance: 28 - 31: 14.739 distance: 31 - 32: 25.751 distance: 32 - 33: 49.864 distance: 33 - 34: 24.904 distance: 34 - 35: 19.133 distance: 35 - 36: 14.464 distance: 35 - 37: 26.303 distance: 40 - 41: 13.211 distance: 40 - 46: 47.788 distance: 42 - 43: 28.595 distance: 43 - 44: 20.890 distance: 44 - 45: 18.262 distance: 46 - 47: 14.967 distance: 47 - 48: 39.942 distance: 47 - 50: 6.888 distance: 48 - 49: 20.922 distance: 48 - 52: 29.952 distance: 50 - 51: 21.971 distance: 51 - 72: 20.251 distance: 52 - 53: 33.437 distance: 53 - 54: 9.684 distance: 53 - 56: 40.071 distance: 54 - 61: 24.595 distance: 56 - 57: 15.488 distance: 57 - 58: 38.935 distance: 58 - 59: 8.677 distance: 61 - 62: 15.460 distance: 62 - 63: 14.121 distance: 62 - 65: 23.763 distance: 63 - 64: 34.296 distance: 63 - 67: 20.445 distance: 65 - 66: 16.853 distance: 67 - 68: 23.234 distance: 68 - 71: 10.264 distance: 69 - 70: 21.986 distance: 69 - 73: 11.324 distance: 71 - 72: 35.685 distance: 73 - 74: 9.320 distance: 73 - 169: 30.358 distance: 74 - 75: 14.234 distance: 74 - 77: 48.226 distance: 75 - 76: 36.249 distance: 75 - 80: 28.864 distance: 76 - 166: 32.589 distance: 77 - 78: 9.082 distance: 77 - 79: 39.855 distance: 80 - 81: 15.555 distance: 81 - 82: 18.770 distance: 81 - 84: 37.487 distance: 82 - 83: 8.978 distance: 84 - 85: 41.752 distance: 85 - 86: 8.197 distance: 86 - 87: 31.092 distance: 86 - 88: 26.047 distance: 90 - 93: 12.203 distance: 91 - 92: 40.907 distance: 93 - 94: 28.255 distance: 94 - 96: 45.211 distance: 97 - 98: 32.635 distance: 98 - 99: 10.103 distance: 98 - 101: 24.976 distance: 99 - 100: 47.055 distance: 99 - 105: 31.360 distance: 101 - 102: 14.539 distance: 102 - 103: 44.586 distance: 102 - 104: 37.410