Starting phenix.real_space_refine on Fri Aug 22 20:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2025/8hr5_34958.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 17 5.16 5 C 4339 2.51 5 N 1351 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7595 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3327 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 9, 'GLU:plan': 25, 'ASP:plan': 11, 'ASN:plan1': 10, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1660 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 3, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 13, 'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 15, 'ASN:plan1': 11, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 200 Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 50, 'rna3p_pyr': 41} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 3 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7595 At special positions: 0 Unit cell: (80.36, 117.26, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 123 15.00 O 1765 8.00 N 1351 7.00 C 4339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 151.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 55.3% alpha, 12.2% beta 42 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 53 removed outlier: 3.616A pdb=" N ARG A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.974A pdb=" N GLU A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 131 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.218A pdb=" N LEU A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.672A pdb=" N ASP A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.620A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 340 removed outlier: 3.517A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.045A pdb=" N LYS A 344 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 345 through 382 removed outlier: 3.618A pdb=" N ASN A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.646A pdb=" N LEU A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'B' and resid 14 through 52 removed outlier: 3.546A pdb=" N TYR B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.944A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 148 removed outlier: 4.314A pdb=" N VAL B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 4.384A pdb=" N SER B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.792A pdb=" N LEU B 206 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.855A pdb=" N HIS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 267 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 216 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 207 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 253 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 302 removed outlier: 5.400A pdb=" N VAL A 289 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 390 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 291 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.521A pdb=" N THR B 201 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 257 " --> pdb=" O THR B 201 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1314 1.33 - 1.45: 2528 1.45 - 1.57: 3856 1.57 - 1.69: 239 1.69 - 1.81: 27 Bond restraints: 7964 Sorted by residual: bond pdb=" O3' A C 79 " pdb=" P U C 80 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.63e+01 bond pdb=" O3' G C 99 " pdb=" P A C 100 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" N VAL A 4 " pdb=" CA VAL A 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.08e+00 bond pdb=" N ILE A 120 " pdb=" CA ILE A 120 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.82e+00 ... (remaining 7959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10921 1.57 - 3.14: 422 3.14 - 4.71: 43 4.71 - 6.28: 10 6.28 - 7.85: 2 Bond angle restraints: 11398 Sorted by residual: angle pdb=" N GLY A 55 " pdb=" CA GLY A 55 " pdb=" C GLY A 55 " ideal model delta sigma weight residual 113.24 107.38 5.86 1.31e+00 5.83e-01 2.00e+01 angle pdb=" N MET A 221 " pdb=" CA MET A 221 " pdb=" C MET A 221 " ideal model delta sigma weight residual 110.80 118.65 -7.85 2.13e+00 2.20e-01 1.36e+01 angle pdb=" C3' G C 91 " pdb=" O3' G C 91 " pdb=" P U C 92 " ideal model delta sigma weight residual 120.20 125.26 -5.06 1.50e+00 4.44e-01 1.14e+01 angle pdb=" N GLU A 222 " pdb=" CA GLU A 222 " pdb=" C GLU A 222 " ideal model delta sigma weight residual 111.39 115.89 -4.50 1.38e+00 5.25e-01 1.06e+01 angle pdb=" CA THR A 10 " pdb=" C THR A 10 " pdb=" O THR A 10 " ideal model delta sigma weight residual 121.33 117.96 3.37 1.08e+00 8.57e-01 9.72e+00 ... (remaining 11393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 4377 35.63 - 71.25: 405 71.25 - 106.88: 27 106.88 - 142.51: 2 142.51 - 178.13: 5 Dihedral angle restraints: 4816 sinusoidal: 2720 harmonic: 2096 Sorted by residual: dihedral pdb=" O4' U C 94 " pdb=" C1' U C 94 " pdb=" N1 U C 94 " pdb=" C2 U C 94 " ideal model delta sinusoidal sigma weight residual 200.00 29.81 170.19 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U C 77 " pdb=" C1' U C 77 " pdb=" N1 U C 77 " pdb=" C2 U C 77 " ideal model delta sinusoidal sigma weight residual 200.00 41.62 158.38 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U C 76 " pdb=" C1' U C 76 " pdb=" N1 U C 76 " pdb=" C2 U C 76 " ideal model delta sinusoidal sigma weight residual 232.00 61.11 170.89 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 4813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1153 0.048 - 0.097: 186 0.097 - 0.145: 49 0.145 - 0.193: 41 0.193 - 0.241: 5 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA MET A 221 " pdb=" N MET A 221 " pdb=" C MET A 221 " pdb=" CB MET A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' G C 91 " pdb=" C4' G C 91 " pdb=" O3' G C 91 " pdb=" C2' G C 91 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A C 207 " pdb=" C4' A C 207 " pdb=" O3' A C 207 " pdb=" C2' A C 207 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1431 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 27 " -0.027 2.00e-02 2.50e+03 1.21e-02 4.41e+00 pdb=" N9 G C 27 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G C 27 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 27 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G C 27 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 27 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 40 " 0.022 2.00e-02 2.50e+03 1.18e-02 3.13e+00 pdb=" N1 C C 40 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 40 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C C 40 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 40 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 40 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C C 40 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C C 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 90 " -0.011 2.00e-02 2.50e+03 1.06e-02 2.52e+00 pdb=" N1 U C 90 " -0.003 2.00e-02 2.50e+03 pdb=" C2 U C 90 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U C 90 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U C 90 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U C 90 " -0.011 2.00e-02 2.50e+03 pdb=" C6 U C 90 " 0.023 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 7314 3.27 - 3.82: 13145 3.82 - 4.36: 14335 4.36 - 4.90: 22495 Nonbonded interactions: 57976 Sorted by model distance: nonbonded pdb=" O2' G C 74 " pdb=" O4' G C 75 " model vdw 2.191 3.040 nonbonded pdb=" O2' A C 71 " pdb=" O4' A C 72 " model vdw 2.195 3.040 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.244 3.040 nonbonded pdb=" O2 U C 87 " pdb=" O6 G C 99 " model vdw 2.246 2.432 nonbonded pdb=" O4 U C 47 " pdb=" O6 G C 68 " model vdw 2.246 2.432 ... (remaining 57971 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.480 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7964 Z= 0.264 Angle : 0.673 7.848 11398 Z= 0.420 Chirality : 0.048 0.241 1434 Planarity : 0.003 0.040 1009 Dihedral : 22.930 178.134 3452 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.37 % Allowed : 2.16 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.32), residues: 699 helix: 1.21 (0.27), residues: 352 sheet: -1.12 (0.55), residues: 90 loop : -1.10 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.018 0.002 TYR A 150 PHE 0.013 0.002 PHE A 370 TRP 0.021 0.002 TRP A 24 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 7964) covalent geometry : angle 0.67269 (11398) hydrogen bonds : bond 0.18117 ( 440) hydrogen bonds : angle 6.44768 ( 1183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.188 Fit side-chains REVERT: B 52 ASN cc_start: 0.8797 (t0) cc_final: 0.8536 (t0) REVERT: B 63 ASP cc_start: 0.5379 (t0) cc_final: 0.5051 (t0) REVERT: B 147 ASP cc_start: 0.8139 (t70) cc_final: 0.7926 (t0) outliers start: 14 outliers final: 1 residues processed: 102 average time/residue: 0.0769 time to fit residues: 10.4196 Evaluate side-chains 71 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.181128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146680 restraints weight = 11532.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146172 restraints weight = 16553.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147095 restraints weight = 13998.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147137 restraints weight = 11460.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147590 restraints weight = 10132.291| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7964 Z= 0.183 Angle : 0.629 9.328 11398 Z= 0.329 Chirality : 0.036 0.182 1434 Planarity : 0.004 0.040 1009 Dihedral : 23.693 172.556 2548 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.32), residues: 699 helix: 2.45 (0.26), residues: 354 sheet: -0.84 (0.51), residues: 103 loop : -1.25 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.022 0.002 TYR A 150 PHE 0.018 0.002 PHE A 370 TRP 0.009 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7964) covalent geometry : angle 0.62949 (11398) hydrogen bonds : bond 0.05617 ( 440) hydrogen bonds : angle 3.83398 ( 1183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.148 Fit side-chains REVERT: B 63 ASP cc_start: 0.6170 (t0) cc_final: 0.5924 (t0) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.0647 time to fit residues: 7.8570 Evaluate side-chains 73 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146672 restraints weight = 11377.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146968 restraints weight = 14269.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148394 restraints weight = 13433.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148081 restraints weight = 10974.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148508 restraints weight = 10901.290| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7964 Z= 0.178 Angle : 0.600 8.305 11398 Z= 0.315 Chirality : 0.036 0.199 1434 Planarity : 0.004 0.038 1009 Dihedral : 23.463 175.032 2547 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.37 % Allowed : 18.27 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.32), residues: 699 helix: 2.88 (0.27), residues: 358 sheet: -0.97 (0.50), residues: 108 loop : -1.21 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.020 0.002 TYR A 150 PHE 0.017 0.002 PHE A 370 TRP 0.005 0.001 TRP A 220 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7964) covalent geometry : angle 0.60001 (11398) hydrogen bonds : bond 0.05635 ( 440) hydrogen bonds : angle 3.64298 ( 1183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.164 Fit side-chains REVERT: B 63 ASP cc_start: 0.6125 (t0) cc_final: 0.5903 (t0) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.0614 time to fit residues: 7.2001 Evaluate side-chains 77 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.182721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150528 restraints weight = 11501.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149963 restraints weight = 14814.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150548 restraints weight = 14190.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150632 restraints weight = 11207.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150777 restraints weight = 10390.273| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7964 Z= 0.144 Angle : 0.551 7.743 11398 Z= 0.291 Chirality : 0.035 0.216 1434 Planarity : 0.003 0.039 1009 Dihedral : 23.275 175.680 2547 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.85 % Allowed : 22.12 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.33), residues: 699 helix: 3.21 (0.26), residues: 358 sheet: -0.92 (0.52), residues: 102 loop : -1.15 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.013 0.001 TYR A 150 PHE 0.013 0.002 PHE A 370 TRP 0.005 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7964) covalent geometry : angle 0.55072 (11398) hydrogen bonds : bond 0.04843 ( 440) hydrogen bonds : angle 3.34651 ( 1183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.190 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.0596 time to fit residues: 7.7343 Evaluate side-chains 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 10 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.173945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137894 restraints weight = 12061.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138239 restraints weight = 12554.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138805 restraints weight = 11089.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139312 restraints weight = 8936.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139481 restraints weight = 8229.049| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7964 Z= 0.154 Angle : 0.560 6.686 11398 Z= 0.296 Chirality : 0.035 0.210 1434 Planarity : 0.003 0.034 1009 Dihedral : 23.251 176.821 2547 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.09 % Allowed : 22.36 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.33), residues: 699 helix: 3.29 (0.27), residues: 359 sheet: -1.03 (0.52), residues: 102 loop : -1.13 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.017 0.002 TYR A 150 PHE 0.016 0.002 PHE A 319 TRP 0.006 0.001 TRP A 24 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7964) covalent geometry : angle 0.56007 (11398) hydrogen bonds : bond 0.05160 ( 440) hydrogen bonds : angle 3.36734 ( 1183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.228 Fit side-chains REVERT: B 192 ASN cc_start: 0.7983 (t0) cc_final: 0.7753 (t0) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.0574 time to fit residues: 6.9415 Evaluate side-chains 78 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130630 restraints weight = 12207.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130976 restraints weight = 12834.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131426 restraints weight = 11356.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131563 restraints weight = 10065.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133587 restraints weight = 8715.235| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 7964 Z= 0.348 Angle : 0.795 8.741 11398 Z= 0.413 Chirality : 0.043 0.180 1434 Planarity : 0.005 0.038 1009 Dihedral : 23.668 177.691 2547 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.45 % Allowed : 19.23 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.32), residues: 699 helix: 2.40 (0.27), residues: 362 sheet: -1.29 (0.49), residues: 109 loop : -1.56 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 134 TYR 0.025 0.003 TYR A 150 PHE 0.031 0.004 PHE A 370 TRP 0.013 0.002 TRP A 24 HIS 0.009 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00779 ( 7964) covalent geometry : angle 0.79472 (11398) hydrogen bonds : bond 0.07717 ( 440) hydrogen bonds : angle 4.06853 ( 1183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.242 Fit side-chains outliers start: 31 outliers final: 22 residues processed: 94 average time/residue: 0.0609 time to fit residues: 8.5991 Evaluate side-chains 86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.172628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137532 restraints weight = 12072.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137864 restraints weight = 12657.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139189 restraints weight = 11528.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139077 restraints weight = 9203.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139506 restraints weight = 8169.000| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7964 Z= 0.142 Angle : 0.558 6.636 11398 Z= 0.299 Chirality : 0.035 0.178 1434 Planarity : 0.003 0.038 1009 Dihedral : 23.378 177.999 2547 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.57 % Allowed : 23.80 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.33), residues: 699 helix: 3.05 (0.27), residues: 359 sheet: -1.17 (0.50), residues: 110 loop : -1.55 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.020 0.002 TYR A 367 PHE 0.018 0.002 PHE A 319 TRP 0.006 0.001 TRP A 24 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7964) covalent geometry : angle 0.55849 (11398) hydrogen bonds : bond 0.05160 ( 440) hydrogen bonds : angle 3.39378 ( 1183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.174 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.0484 time to fit residues: 6.3259 Evaluate side-chains 77 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.172389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138226 restraints weight = 12070.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138215 restraints weight = 14103.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139481 restraints weight = 13905.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139486 restraints weight = 10689.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139849 restraints weight = 11366.257| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7964 Z= 0.171 Angle : 0.584 6.818 11398 Z= 0.311 Chirality : 0.036 0.167 1434 Planarity : 0.003 0.035 1009 Dihedral : 23.343 178.514 2547 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.05 % Allowed : 24.76 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.33), residues: 699 helix: 3.07 (0.27), residues: 360 sheet: -1.19 (0.49), residues: 113 loop : -1.57 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.019 0.002 TYR A 367 PHE 0.016 0.002 PHE A 319 TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7964) covalent geometry : angle 0.58435 (11398) hydrogen bonds : bond 0.05541 ( 440) hydrogen bonds : angle 3.42329 ( 1183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.134 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.0536 time to fit residues: 6.8476 Evaluate side-chains 79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.172608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137380 restraints weight = 11956.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137728 restraints weight = 12045.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138448 restraints weight = 10853.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138659 restraints weight = 8952.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138915 restraints weight = 8222.319| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7964 Z= 0.171 Angle : 0.584 6.824 11398 Z= 0.310 Chirality : 0.036 0.173 1434 Planarity : 0.003 0.036 1009 Dihedral : 23.338 178.923 2547 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.29 % Allowed : 24.52 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.33), residues: 699 helix: 3.11 (0.27), residues: 360 sheet: -1.18 (0.50), residues: 112 loop : -1.56 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.019 0.002 TYR A 367 PHE 0.016 0.002 PHE A 319 TRP 0.007 0.001 TRP A 24 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7964) covalent geometry : angle 0.58420 (11398) hydrogen bonds : bond 0.05494 ( 440) hydrogen bonds : angle 3.40189 ( 1183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.151 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 77 average time/residue: 0.0551 time to fit residues: 6.5530 Evaluate side-chains 82 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.175518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141704 restraints weight = 11914.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141091 restraints weight = 14095.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142105 restraints weight = 12232.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142141 restraints weight = 10260.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142545 restraints weight = 9346.040| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7964 Z= 0.134 Angle : 0.540 6.318 11398 Z= 0.288 Chirality : 0.035 0.195 1434 Planarity : 0.003 0.035 1009 Dihedral : 23.273 178.457 2547 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.81 % Allowed : 25.72 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.33), residues: 699 helix: 3.33 (0.26), residues: 362 sheet: -1.04 (0.49), residues: 116 loop : -1.52 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.020 0.002 TYR A 252 PHE 0.016 0.002 PHE A 319 TRP 0.007 0.001 TRP A 24 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7964) covalent geometry : angle 0.54034 (11398) hydrogen bonds : bond 0.04752 ( 440) hydrogen bonds : angle 3.14639 ( 1183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.197 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 83 average time/residue: 0.0525 time to fit residues: 6.9105 Evaluate side-chains 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.175951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140714 restraints weight = 11997.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140629 restraints weight = 11970.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141464 restraints weight = 10549.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141648 restraints weight = 8838.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141900 restraints weight = 8103.201| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7964 Z= 0.128 Angle : 0.536 6.245 11398 Z= 0.286 Chirality : 0.034 0.196 1434 Planarity : 0.003 0.034 1009 Dihedral : 23.243 178.515 2547 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.33 % Allowed : 26.20 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.34), residues: 699 helix: 3.45 (0.26), residues: 362 sheet: -0.96 (0.49), residues: 116 loop : -1.47 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.018 0.001 TYR A 367 PHE 0.020 0.002 PHE A 319 TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7964) covalent geometry : angle 0.53600 (11398) hydrogen bonds : bond 0.04645 ( 440) hydrogen bonds : angle 3.08518 ( 1183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1054.11 seconds wall clock time: 18 minutes 55.50 seconds (1135.50 seconds total)