Starting phenix.real_space_refine on Tue Feb 11 03:28:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.map" model { file = "/net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soa_25264/02_2025/7soa_25264.cif" } resolution = 3.1 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= -0.002 sd= 0.112 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 15 5.16 5 C 2476 2.51 5 N 620 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3850 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1994 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 234} Chain breaks: 5 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.45, per 1000 atoms: 1.68 Number of scatterers: 3850 At special positions: 0 Unit cell: (63.225, 85.143, 76.713, 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 15 16.00 O 739 8.00 N 620 7.00 C 2476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 280 " " NAG A1303 " - " ASN A 163 " " NAG A1304 " - " ASN A 232 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 464.6 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 4.2% alpha, 55.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.970A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.681A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 262 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR A 95 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.386A pdb=" N THR A 272 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP A 288 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 274 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 286 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 276 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.990A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.614A pdb=" N PHE A 236 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.010A pdb=" N ASN A 137 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR A 238 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 240 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 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: 1.15 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 722 1.33 - 1.45: 1076 1.45 - 1.57: 2128 1.57 - 1.70: 2 1.70 - 1.82: 20 Bond restraints: 3948 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.22e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.38e+00 ... (remaining 3943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 4971 2.21 - 4.41: 327 4.41 - 6.62: 54 6.62 - 8.82: 11 8.82 - 11.03: 1 Bond angle restraints: 5364 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 angle pdb=" C LEU A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 120.03 127.11 -7.08 9.90e-01 1.02e+00 5.11e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.00 -7.15 1.01e+00 9.80e-01 5.01e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 5359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2277 17.19 - 34.39: 83 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2384 sinusoidal: 998 harmonic: 1386 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.58 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" C LYS A 185 " pdb=" N LYS A 185 " pdb=" CA LYS A 185 " pdb=" CB LYS A 185 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CB GLU A 189 " pdb=" CG GLU A 189 " pdb=" CD GLU A 189 " pdb=" OE1 GLU A 189 " ideal model delta sinusoidal sigma weight residual 0.00 85.96 -85.96 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 485 0.095 - 0.190: 94 0.190 - 0.285: 16 0.285 - 0.380: 8 0.380 - 0.475: 1 Chirality restraints: 604 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA LYS A 185 " pdb=" N LYS A 185 " pdb=" C LYS A 185 " pdb=" CB LYS A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 601 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.242 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG A1304 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 34 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ARG A 34 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY A 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 104 " -0.031 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR H 104 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR H 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 104 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR H 104 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 104 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 104 " -0.026 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 205 2.73 - 3.28: 3456 3.28 - 3.82: 6166 3.82 - 4.36: 8061 4.36 - 4.90: 13416 Nonbonded interactions: 31304 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.194 3.040 nonbonded pdb=" N THR A 29 " pdb=" O THR A 29 " model vdw 2.551 2.496 nonbonded pdb=" N SER A 151 " pdb=" O SER A 151 " model vdw 2.556 2.496 nonbonded pdb=" N GLY A 156 " pdb=" N VAL A 157 " model vdw 2.588 2.560 nonbonded pdb=" O ASP L 92 " pdb=" NH1 ARG H 103 " model vdw 2.595 3.120 ... (remaining 31299 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: 8.250 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.370 Find NCS groups from input model: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 0.062 3948 Z= 0.695 Angle : 1.273 11.028 5364 Z= 0.860 Chirality : 0.085 0.475 604 Planarity : 0.010 0.208 675 Dihedral : 10.148 85.964 1481 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.99 (0.37), residues: 461 helix: 0.55 (1.59), residues: 11 sheet: 1.38 (0.37), residues: 184 loop : 0.20 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP H 47 HIS 0.001 0.001 HIS A 66 PHE 0.018 0.003 PHE A 55 TYR 0.031 0.004 TYR H 104 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.397 Fit side-chains REVERT: A 154 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7276 (tp30) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1921 time to fit residues: 19.4578 Evaluate side-chains 57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096944 restraints weight = 4202.184| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.27 r_work: 0.3034 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3948 Z= 0.297 Angle : 0.658 13.212 5364 Z= 0.333 Chirality : 0.047 0.150 604 Planarity : 0.005 0.046 675 Dihedral : 6.702 57.213 644 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.94 % Allowed : 6.07 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.38), residues: 461 helix: 2.81 (1.61), residues: 11 sheet: 1.41 (0.36), residues: 193 loop : 0.18 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS A 66 PHE 0.016 0.002 PHE H 50 TYR 0.016 0.002 TYR H 95 ARG 0.005 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: H 17 SER cc_start: 0.8350 (p) cc_final: 0.8079 (t) REVERT: A 125 ASN cc_start: 0.8349 (m110) cc_final: 0.8136 (m110) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1538 time to fit residues: 11.8911 Evaluate side-chains 53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117757 restraints weight = 3945.981| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.08 r_work: 0.3082 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3948 Z= 0.192 Angle : 0.533 7.078 5364 Z= 0.279 Chirality : 0.045 0.142 604 Planarity : 0.004 0.039 675 Dihedral : 4.614 26.551 641 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 6.80 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.39), residues: 461 helix: 3.19 (1.70), residues: 11 sheet: 1.64 (0.37), residues: 190 loop : 0.01 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 133 TYR 0.014 0.001 TYR A 168 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: H 17 SER cc_start: 0.8438 (p) cc_final: 0.8173 (t) REVERT: A 125 ASN cc_start: 0.8378 (m110) cc_final: 0.8176 (m110) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.1673 time to fit residues: 12.7458 Evaluate side-chains 55 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 60.4126 > 50: distance: 85 - 92: 8.818 distance: 92 - 93: 14.639 distance: 92 - 158: 29.227 distance: 93 - 94: 28.390 distance: 93 - 96: 24.668 distance: 94 - 95: 26.397 distance: 94 - 101: 39.775 distance: 96 - 97: 20.986 distance: 97 - 98: 14.029 distance: 98 - 99: 28.511 distance: 98 - 100: 6.738 distance: 101 - 102: 34.164 distance: 102 - 103: 33.501 distance: 102 - 105: 39.830 distance: 103 - 104: 30.846 distance: 103 - 113: 39.634 distance: 105 - 106: 17.512 distance: 106 - 107: 11.230 distance: 106 - 108: 16.258 distance: 107 - 109: 13.225 distance: 108 - 110: 24.605 distance: 109 - 111: 26.168 distance: 110 - 111: 29.572 distance: 111 - 112: 24.866 distance: 113 - 114: 32.698 distance: 114 - 115: 42.884 distance: 114 - 117: 16.295 distance: 115 - 116: 39.337 distance: 115 - 121: 40.637 distance: 117 - 118: 19.893 distance: 118 - 119: 5.817 distance: 121 - 122: 28.677 distance: 122 - 123: 34.698 distance: 122 - 125: 20.055 distance: 123 - 124: 29.387 distance: 123 - 129: 24.340 distance: 125 - 126: 30.982 distance: 126 - 127: 19.323 distance: 126 - 128: 10.489 distance: 129 - 130: 32.370 distance: 130 - 131: 40.672 distance: 130 - 133: 46.958 distance: 131 - 132: 36.739 distance: 131 - 137: 29.592 distance: 133 - 134: 10.791 distance: 134 - 135: 8.952 distance: 134 - 136: 14.240 distance: 137 - 138: 16.018 distance: 137 - 143: 16.427 distance: 138 - 139: 25.092 distance: 138 - 141: 11.212 distance: 139 - 140: 33.850 distance: 139 - 144: 20.389 distance: 141 - 142: 6.732 distance: 142 - 143: 28.734 distance: 144 - 145: 25.428 distance: 145 - 146: 22.778 distance: 145 - 148: 22.119 distance: 146 - 147: 14.399 distance: 146 - 155: 40.019 distance: 148 - 149: 25.389 distance: 149 - 150: 8.613 distance: 149 - 151: 7.950 distance: 150 - 152: 17.804 distance: 151 - 153: 10.798 distance: 152 - 154: 9.081 distance: 153 - 154: 17.974 distance: 155 - 156: 8.450 distance: 156 - 157: 22.481 distance: 156 - 159: 23.302 distance: 157 - 158: 31.510 distance: 157 - 162: 5.929 distance: 159 - 160: 16.366 distance: 159 - 161: 12.433 distance: 162 - 163: 5.361 distance: 163 - 164: 21.318 distance: 163 - 166: 14.458 distance: 164 - 165: 24.331 distance: 164 - 173: 39.088 distance: 166 - 167: 8.600 distance: 167 - 168: 5.616 distance: 167 - 169: 16.090 distance: 168 - 170: 6.877 distance: 170 - 172: 19.718 distance: 171 - 172: 38.361 distance: 173 - 174: 27.320 distance: 174 - 175: 10.722 distance: 175 - 176: 10.105 distance: 175 - 177: 8.471