Starting phenix.real_space_refine on Tue May 13 21:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.map" model { file = "/net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hq7_34946/05_2025/8hq7_34946.cif" } resolution = 2.7 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= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3142 atoms to isotropic. 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 34 5.16 5 C 5221 2.51 5 N 1387 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "M" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} 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 Time building chain proxies: 6.84, per 1000 atoms: 0.82 Number of scatterers: 8292 At special positions: 0 Unit cell: (136.96, 93.304, 124.12, 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 34 16.00 O 1650 8.00 N 1387 7.00 C 5221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 997.9 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 9.7% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.709A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.957A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.428A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.071A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.233A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 129 removed outlier: 4.058A pdb=" N SER N 129 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.988A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.560A pdb=" N ASN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.160A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.089A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.089A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER M 99 " --> pdb=" O PHE M 109 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE M 109 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 129 through 133 removed outlier: 6.023A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 129 through 133 removed outlier: 6.023A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.574A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.942A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13 removed outlier: 4.014A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 116 through 120 removed outlier: 6.137A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.171A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.529A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.413A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.413A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 192 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.849A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.989A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.915A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 146 through 151 361 hydrogen bonds defined for protein. 891 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: 2.93 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2658 1.35 - 1.47: 2174 1.47 - 1.59: 3621 1.59 - 1.71: 0 1.71 - 1.83: 40 Bond restraints: 8493 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.78e-02 3.16e+03 1.50e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG B 2 " pdb=" O3 NAG B 2 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 8488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 11523 3.96 - 7.91: 33 7.91 - 11.87: 2 11.87 - 15.82: 0 15.82 - 19.78: 2 Bond angle restraints: 11560 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 134.18 -19.78 2.30e+00 1.89e-01 7.40e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 133.94 -19.54 2.30e+00 1.89e-01 7.22e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.99 117.53 -8.54 1.57e+00 4.06e-01 2.96e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 108.60 115.16 -6.56 1.46e+00 4.69e-01 2.02e+01 angle pdb=" C PRO H 14 " pdb=" N THR H 15 " pdb=" CA THR H 15 " ideal model delta sigma weight residual 122.08 127.66 -5.58 1.47e+00 4.63e-01 1.44e+01 ... (remaining 11555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4661 16.21 - 32.42: 331 32.42 - 48.62: 80 48.62 - 64.83: 20 64.83 - 81.04: 12 Dihedral angle restraints: 5104 sinusoidal: 1980 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual 180.00 -130.92 -49.08 0 5.00e+00 4.00e-02 9.64e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -4.96 -81.04 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS M 149 " pdb=" SG CYS M 149 " pdb=" SG CYS M 205 " pdb=" CB CYS M 205 " ideal model delta sinusoidal sigma weight residual 93.00 173.58 -80.58 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1181 0.083 - 0.167: 114 0.167 - 0.250: 1 0.250 - 0.333: 1 0.333 - 0.417: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA THR H 15 " pdb=" N THR H 15 " pdb=" C THR H 15 " pdb=" CB THR H 15 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1295 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 116 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO H 117 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 157 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO M 158 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 80 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO L 81 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " 0.027 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 141 2.68 - 3.24: 7354 3.24 - 3.79: 12087 3.79 - 4.35: 16965 4.35 - 4.90: 28668 Nonbonded interactions: 65215 Sorted by model distance: nonbonded pdb=" OG SER L 163 " pdb=" OG SER L 177 " model vdw 2.131 3.040 nonbonded pdb=" OD2 ASP N 172 " pdb=" OG1 THR N 174 " model vdw 2.141 3.040 nonbonded pdb=" CB CYS A 379 " pdb=" CB CYS A 432 " model vdw 2.212 3.072 nonbonded pdb=" OD1 ASP M 61 " pdb=" NH2 ARG N 96 " model vdw 2.291 3.120 nonbonded pdb=" OG1 THR M 200 " pdb=" OE1 GLN M 201 " model vdw 2.301 3.040 ... (remaining 65210 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: 6.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.003 0.033 8509 Z= 0.152 Angle : 0.738 19.780 11594 Z= 0.379 Chirality : 0.047 0.417 1298 Planarity : 0.006 0.086 1487 Dihedral : 12.536 77.415 3066 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: 0.23 (0.26), residues: 1072 helix: -2.67 (0.55), residues: 57 sheet: 1.41 (0.25), residues: 452 loop : -0.61 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 118 HIS 0.004 0.001 HIS N 191 PHE 0.011 0.001 PHE N 211 TYR 0.015 0.002 TYR H 160 ARG 0.004 0.000 ARG H 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.09992 ( 3) link_BETA1-4 : bond 0.00232 ( 1) link_BETA1-4 : angle 0.99809 ( 3) hydrogen bonds : bond 0.10947 ( 317) hydrogen bonds : angle 6.52206 ( 891) SS BOND : bond 0.00837 ( 14) SS BOND : angle 3.38717 ( 28) covalent geometry : bond 0.00342 ( 8493) covalent geometry : angle 0.71975 (11560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: M 208 ASN cc_start: 0.7153 (m110) cc_final: 0.6844 (m110) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 1.6172 time to fit residues: 199.8448 Evaluate side-chains 94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS M 13 GLN M 208 ASN N 162 GLN L 125 GLN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105518 restraints weight = 13124.076| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.31 r_work: 0.3244 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8509 Z= 0.153 Angle : 0.671 14.768 11594 Z= 0.348 Chirality : 0.046 0.225 1298 Planarity : 0.006 0.083 1487 Dihedral : 5.526 55.441 1209 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.28 % Allowed : 6.42 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.25 (0.26), residues: 1072 helix: -2.73 (0.52), residues: 58 sheet: 1.47 (0.25), residues: 449 loop : -0.63 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 150 HIS 0.007 0.001 HIS A 519 PHE 0.011 0.001 PHE N 211 TYR 0.015 0.002 TYR N 194 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 1.16767 ( 3) link_BETA1-4 : bond 0.00236 ( 1) link_BETA1-4 : angle 1.11232 ( 3) hydrogen bonds : bond 0.03967 ( 317) hydrogen bonds : angle 5.65644 ( 891) SS BOND : bond 0.00687 ( 14) SS BOND : angle 2.64568 ( 28) covalent geometry : bond 0.00361 ( 8493) covalent geometry : angle 0.65858 (11560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8672 (mttp) REVERT: M 208 ASN cc_start: 0.7269 (m-40) cc_final: 0.6988 (m110) REVERT: H 105 ASP cc_start: 0.8250 (p0) cc_final: 0.7973 (p0) REVERT: L 18 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7765 (ttm-80) REVERT: L 166 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5563 (pp20) outliers start: 12 outliers final: 2 residues processed: 97 average time/residue: 1.5431 time to fit residues: 157.4645 Evaluate side-chains 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS N 162 GLN N 191 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106520 restraints weight = 13349.744| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.34 r_work: 0.3262 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8509 Z= 0.117 Angle : 0.619 14.665 11594 Z= 0.320 Chirality : 0.044 0.217 1298 Planarity : 0.005 0.078 1487 Dihedral : 5.173 51.362 1209 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.50 % Allowed : 10.05 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1072 helix: -2.80 (0.53), residues: 57 sheet: 1.44 (0.25), residues: 464 loop : -0.52 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 118 HIS 0.007 0.001 HIS A 519 PHE 0.008 0.001 PHE N 211 TYR 0.012 0.001 TYR H 160 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.08984 ( 3) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.16129 ( 3) hydrogen bonds : bond 0.03524 ( 317) hydrogen bonds : angle 5.45052 ( 891) SS BOND : bond 0.00555 ( 14) SS BOND : angle 2.44670 ( 28) covalent geometry : bond 0.00267 ( 8493) covalent geometry : angle 0.60731 (11560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8666 (mttp) REVERT: M 208 ASN cc_start: 0.7206 (m-40) cc_final: 0.6989 (m110) REVERT: M 215 LYS cc_start: 0.5441 (mmtm) cc_final: 0.4699 (tptt) REVERT: N 191 HIS cc_start: 0.4074 (m-70) cc_final: 0.3852 (m-70) REVERT: H 105 ASP cc_start: 0.7986 (p0) cc_final: 0.7550 (p0) REVERT: L 18 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7622 (ttm-80) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 1.6585 time to fit residues: 167.1291 Evaluate side-chains 87 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 109 LYS Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 0.0870 chunk 61 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.145255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105767 restraints weight = 13344.510| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.30 r_work: 0.3273 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8509 Z= 0.122 Angle : 0.614 11.691 11594 Z= 0.319 Chirality : 0.044 0.198 1298 Planarity : 0.005 0.077 1487 Dihedral : 5.007 46.829 1209 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.03 % Allowed : 10.59 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1072 helix: -2.74 (0.54), residues: 57 sheet: 1.47 (0.25), residues: 458 loop : -0.53 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.008 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.012 0.001 TYR H 96 ARG 0.005 0.000 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 1.06816 ( 3) link_BETA1-4 : bond 0.00256 ( 1) link_BETA1-4 : angle 1.21910 ( 3) hydrogen bonds : bond 0.03531 ( 317) hydrogen bonds : angle 5.34202 ( 891) SS BOND : bond 0.00554 ( 14) SS BOND : angle 2.37527 ( 28) covalent geometry : bond 0.00282 ( 8493) covalent geometry : angle 0.60319 (11560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: M 75 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8654 (mttp) REVERT: M 215 LYS cc_start: 0.5434 (mmtm) cc_final: 0.4703 (tptt) REVERT: N 79 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: N 191 HIS cc_start: 0.4122 (m-70) cc_final: 0.3892 (m-70) REVERT: H 105 ASP cc_start: 0.7974 (p0) cc_final: 0.7595 (p0) REVERT: L 18 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7625 (ttm-80) REVERT: L 195 CYS cc_start: 0.4561 (OUTLIER) cc_final: 0.4200 (t) outliers start: 19 outliers final: 4 residues processed: 98 average time/residue: 1.5265 time to fit residues: 157.4542 Evaluate side-chains 89 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 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 360 ASN A 519 HIS H 212 ASN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106247 restraints weight = 13227.079| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.32 r_work: 0.3261 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8509 Z= 0.124 Angle : 0.621 15.969 11594 Z= 0.321 Chirality : 0.045 0.247 1298 Planarity : 0.005 0.076 1487 Dihedral : 4.870 46.593 1209 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.67 % Allowed : 11.55 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1072 helix: -2.72 (0.55), residues: 57 sheet: 1.69 (0.26), residues: 428 loop : -0.62 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 118 HIS 0.008 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.012 0.001 TYR H 96 ARG 0.004 0.000 ARG L 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 1.05082 ( 3) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 1.32333 ( 3) hydrogen bonds : bond 0.03526 ( 317) hydrogen bonds : angle 5.30310 ( 891) SS BOND : bond 0.00648 ( 14) SS BOND : angle 2.43225 ( 28) covalent geometry : bond 0.00289 ( 8493) covalent geometry : angle 0.60999 (11560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: M 3 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: M 75 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (mttp) REVERT: M 215 LYS cc_start: 0.5287 (mmtm) cc_final: 0.4690 (tptt) REVERT: N 191 HIS cc_start: 0.4154 (m-70) cc_final: 0.3938 (m-70) REVERT: L 18 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: L 166 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5274 (pp20) REVERT: L 195 CYS cc_start: 0.4586 (OUTLIER) cc_final: 0.4234 (t) outliers start: 25 outliers final: 5 residues processed: 95 average time/residue: 1.5387 time to fit residues: 154.1357 Evaluate side-chains 88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** 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 = 0.3967 r_free = 0.3967 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105184 restraints weight = 13204.036| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.26 r_work: 0.3262 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8509 Z= 0.137 Angle : 0.637 13.724 11594 Z= 0.330 Chirality : 0.045 0.241 1298 Planarity : 0.005 0.077 1487 Dihedral : 4.820 47.504 1209 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.14 % Allowed : 12.73 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.30 (0.26), residues: 1072 helix: -2.75 (0.55), residues: 57 sheet: 1.57 (0.25), residues: 449 loop : -0.65 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 150 HIS 0.009 0.001 HIS A 519 PHE 0.010 0.001 PHE N 211 TYR 0.014 0.001 TYR H 96 ARG 0.007 0.000 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.07159 ( 3) link_BETA1-4 : bond 0.00295 ( 1) link_BETA1-4 : angle 1.42620 ( 3) hydrogen bonds : bond 0.03661 ( 317) hydrogen bonds : angle 5.34205 ( 891) SS BOND : bond 0.00664 ( 14) SS BOND : angle 2.52970 ( 28) covalent geometry : bond 0.00323 ( 8493) covalent geometry : angle 0.62528 (11560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 SER cc_start: 0.8342 (m) cc_final: 0.8113 (p) REVERT: M 3 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: M 75 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (mttp) REVERT: M 215 LYS cc_start: 0.5293 (mmtm) cc_final: 0.4686 (tptt) REVERT: N 191 HIS cc_start: 0.4365 (m-70) cc_final: 0.4090 (m-70) REVERT: H 105 ASP cc_start: 0.8058 (p0) cc_final: 0.7691 (p0) REVERT: L 78 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6179 (tpt-90) REVERT: L 166 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5295 (pp20) REVERT: L 195 CYS cc_start: 0.4764 (OUTLIER) cc_final: 0.4523 (t) outliers start: 20 outliers final: 5 residues processed: 95 average time/residue: 1.4697 time to fit residues: 147.2215 Evaluate side-chains 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 63 optimal weight: 0.0870 chunk 46 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS H 16 GLN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106818 restraints weight = 13224.518| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.26 r_work: 0.3289 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8509 Z= 0.108 Angle : 0.609 15.805 11594 Z= 0.314 Chirality : 0.044 0.245 1298 Planarity : 0.005 0.073 1487 Dihedral : 4.552 45.475 1209 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.93 % Allowed : 13.69 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.42 (0.26), residues: 1072 helix: -2.69 (0.56), residues: 57 sheet: 1.75 (0.26), residues: 428 loop : -0.57 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.009 0.001 HIS A 519 PHE 0.008 0.001 PHE N 211 TYR 0.010 0.001 TYR H 96 ARG 0.005 0.000 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 0.98901 ( 3) link_BETA1-4 : bond 0.00325 ( 1) link_BETA1-4 : angle 1.40291 ( 3) hydrogen bonds : bond 0.03266 ( 317) hydrogen bonds : angle 5.21652 ( 891) SS BOND : bond 0.00560 ( 14) SS BOND : angle 2.46340 ( 28) covalent geometry : bond 0.00245 ( 8493) covalent geometry : angle 0.59662 (11560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 366 SER cc_start: 0.8352 (m) cc_final: 0.8104 (p) REVERT: M 75 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8652 (mttp) REVERT: M 215 LYS cc_start: 0.5303 (mmtm) cc_final: 0.4739 (tptt) REVERT: N 191 HIS cc_start: 0.4176 (m-70) cc_final: 0.3967 (m-70) REVERT: L 18 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7443 (ttm-80) REVERT: L 78 ARG cc_start: 0.7032 (mmm160) cc_final: 0.6014 (tpt-90) REVERT: L 195 CYS cc_start: 0.4716 (OUTLIER) cc_final: 0.4480 (t) outliers start: 18 outliers final: 5 residues processed: 95 average time/residue: 1.5275 time to fit residues: 152.8590 Evaluate side-chains 92 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.145268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106140 restraints weight = 13408.516| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.25 r_work: 0.3276 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8509 Z= 0.123 Angle : 0.633 15.393 11594 Z= 0.327 Chirality : 0.045 0.267 1298 Planarity : 0.005 0.074 1487 Dihedral : 4.628 45.315 1209 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.93 % Allowed : 13.69 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.33 (0.26), residues: 1072 helix: -2.75 (0.55), residues: 57 sheet: 1.71 (0.26), residues: 428 loop : -0.64 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 118 HIS 0.009 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.012 0.001 TYR H 96 ARG 0.004 0.000 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 1.04311 ( 3) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.36109 ( 3) hydrogen bonds : bond 0.03440 ( 317) hydrogen bonds : angle 5.19618 ( 891) SS BOND : bond 0.00694 ( 14) SS BOND : angle 2.68343 ( 28) covalent geometry : bond 0.00287 ( 8493) covalent geometry : angle 0.61936 (11560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 SER cc_start: 0.8356 (m) cc_final: 0.8119 (p) REVERT: M 75 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8649 (mttp) REVERT: M 215 LYS cc_start: 0.5341 (mmtm) cc_final: 0.4745 (tptt) REVERT: N 191 HIS cc_start: 0.4228 (m-70) cc_final: 0.4006 (m-70) REVERT: L 78 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6046 (tpt-90) REVERT: L 166 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5320 (pp20) REVERT: L 195 CYS cc_start: 0.4757 (OUTLIER) cc_final: 0.4534 (t) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 1.5555 time to fit residues: 154.1241 Evaluate side-chains 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 519 HIS ** L 211 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.145459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106586 restraints weight = 13429.720| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.33 r_work: 0.3269 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8509 Z= 0.120 Angle : 0.630 15.755 11594 Z= 0.326 Chirality : 0.045 0.243 1298 Planarity : 0.005 0.073 1487 Dihedral : 4.612 44.614 1209 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.60 % Allowed : 14.01 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.33 (0.26), residues: 1072 helix: -2.85 (0.55), residues: 57 sheet: 1.72 (0.26), residues: 428 loop : -0.64 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 118 HIS 0.010 0.001 HIS A 519 PHE 0.009 0.001 PHE N 211 TYR 0.011 0.001 TYR H 96 ARG 0.005 0.000 ARG N 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.04301 ( 3) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 1.29848 ( 3) hydrogen bonds : bond 0.03385 ( 317) hydrogen bonds : angle 5.18170 ( 891) SS BOND : bond 0.00653 ( 14) SS BOND : angle 2.65467 ( 28) covalent geometry : bond 0.00281 ( 8493) covalent geometry : angle 0.61713 (11560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 SER cc_start: 0.8363 (m) cc_final: 0.8122 (p) REVERT: M 75 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8660 (mttp) REVERT: M 215 LYS cc_start: 0.5267 (mmtm) cc_final: 0.4728 (tptt) REVERT: H 16 GLN cc_start: 0.6801 (mp10) cc_final: 0.6551 (mp10) REVERT: L 78 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6068 (tpt-90) REVERT: L 166 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5355 (pp20) REVERT: L 195 CYS cc_start: 0.4729 (OUTLIER) cc_final: 0.4508 (t) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 1.5055 time to fit residues: 142.6621 Evaluate side-chains 89 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 195 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 56.0109 > 50: distance: 69 - 89: 4.152 distance: 85 - 89: 4.193 distance: 89 - 90: 19.376 distance: 90 - 91: 33.113 distance: 90 - 93: 26.675 distance: 91 - 92: 19.452 distance: 91 - 97: 26.378 distance: 93 - 94: 6.984 distance: 94 - 95: 5.532 distance: 97 - 98: 19.005 distance: 98 - 99: 16.013 distance: 98 - 101: 5.415 distance: 99 - 100: 30.877 distance: 99 - 109: 7.872 distance: 101 - 102: 6.265 distance: 102 - 103: 3.243 distance: 103 - 105: 7.022 distance: 104 - 106: 5.043 distance: 106 - 107: 3.629 distance: 107 - 108: 5.029 distance: 109 - 110: 19.790 distance: 110 - 111: 29.548 distance: 110 - 113: 16.020 distance: 111 - 112: 17.496 distance: 111 - 118: 33.840 distance: 113 - 114: 23.015 distance: 114 - 115: 15.316 distance: 115 - 116: 8.619 distance: 116 - 117: 7.601 distance: 118 - 119: 36.581 distance: 119 - 120: 38.535 distance: 119 - 122: 47.180 distance: 120 - 121: 14.313 distance: 120 - 126: 16.403 distance: 122 - 123: 45.642 distance: 123 - 124: 21.407 distance: 123 - 125: 23.966 distance: 126 - 127: 8.302 distance: 126 - 132: 14.379 distance: 127 - 128: 17.731 distance: 127 - 130: 17.379 distance: 128 - 129: 37.136 distance: 128 - 133: 23.868 distance: 130 - 131: 8.328 distance: 131 - 132: 35.372 distance: 133 - 134: 37.515 distance: 134 - 135: 17.505 distance: 134 - 137: 8.999 distance: 135 - 136: 38.891 distance: 135 - 141: 11.406 distance: 137 - 138: 27.070 distance: 138 - 139: 24.708 distance: 138 - 140: 46.433 distance: 141 - 142: 19.450 distance: 142 - 143: 20.221 distance: 142 - 145: 28.691 distance: 143 - 144: 40.259 distance: 143 - 149: 22.137 distance: 145 - 146: 36.366 distance: 146 - 147: 55.543 distance: 146 - 148: 49.862 distance: 149 - 150: 16.913 distance: 150 - 151: 22.319 distance: 150 - 153: 31.774 distance: 151 - 152: 21.695 distance: 151 - 160: 25.756 distance: 153 - 154: 22.879 distance: 154 - 155: 26.978 distance: 154 - 156: 23.215 distance: 155 - 157: 30.453 distance: 156 - 158: 20.523 distance: 158 - 159: 3.696 distance: 160 - 161: 16.367 distance: 161 - 162: 12.666 distance: 161 - 164: 18.843 distance: 162 - 163: 32.750 distance: 162 - 167: 46.059 distance: 164 - 165: 45.957 distance: 164 - 166: 22.037 distance: 167 - 168: 21.559 distance: 168 - 169: 7.583 distance: 169 - 170: 6.482 distance: 169 - 171: 25.730