Starting phenix.real_space_refine on Wed Feb 12 11:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr5_34958/02_2025/8hr5_34958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr5_34958/02_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_34958/02_2025/8hr5_34958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr5_34958/02_2025/8hr5_34958.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr5_34958/02_2025/8hr5_34958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr5_34958/02_2025/8hr5_34958.cif" } resolution = 3.73 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= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 9, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'GLU:plan': 25, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} 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: 6.18, per 1000 atoms: 0.81 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: 2.63 Conformation dependent library (CDL) restraints added in 715.6 milliseconds 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: 2.70 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: 2.92 Time building geometry restraints manager: 2.67 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: 4.690 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- 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= 0.282 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 (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: 0.07 (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 TRP 0.021 0.002 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.013 0.002 PHE A 370 TYR 0.018 0.002 TYR A 150 ARG 0.002 0.000 ARG A 404 *********************** 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 : 0.679 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: 0.2247 time to fit residues: 30.3462 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 : 0.695 ------------------------------------------------------------------------------- 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 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.180289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146436 restraints weight = 11426.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145902 restraints weight = 17728.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146597 restraints weight = 14371.021| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7964 Z= 0.270 Angle : 0.645 9.566 11398 Z= 0.336 Chirality : 0.037 0.183 1434 Planarity : 0.004 0.041 1009 Dihedral : 23.687 172.644 2548 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.16 % Allowed : 14.42 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.32), residues: 699 helix: 2.39 (0.27), residues: 356 sheet: -0.91 (0.50), residues: 103 loop : -1.21 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 PHE 0.020 0.003 PHE A 370 TYR 0.023 0.002 TYR A 150 ARG 0.007 0.001 ARG B 134 *********************** 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 89 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.633 Fit side-chains REVERT: B 63 ASP cc_start: 0.6193 (t0) cc_final: 0.5950 (t0) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.1519 time to fit residues: 18.3333 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 : 0.680 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 50.0000 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.181357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150134 restraints weight = 11544.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149467 restraints weight = 17092.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149954 restraints weight = 14256.298| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7964 Z= 0.227 Angle : 0.585 8.337 11398 Z= 0.308 Chirality : 0.036 0.204 1434 Planarity : 0.004 0.036 1009 Dihedral : 23.430 175.242 2547 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.33), residues: 699 helix: 2.96 (0.27), residues: 358 sheet: -0.98 (0.51), residues: 102 loop : -1.10 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 220 HIS 0.004 0.001 HIS A 160 PHE 0.015 0.002 PHE A 370 TYR 0.019 0.002 TYR A 417 ARG 0.008 0.001 ARG B 134 *********************** 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 86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.615 Fit side-chains REVERT: B 63 ASP cc_start: 0.6153 (t0) cc_final: 0.5952 (t0) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1489 time to fit residues: 17.4133 Evaluate side-chains 75 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 393 SER 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 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.175349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137132 restraints weight = 11946.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139739 restraints weight = 10375.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140019 restraints weight = 7339.695| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7964 Z= 0.184 Angle : 0.539 7.456 11398 Z= 0.285 Chirality : 0.034 0.217 1434 Planarity : 0.003 0.035 1009 Dihedral : 23.234 175.866 2547 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.81 % Allowed : 20.67 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.33), residues: 699 helix: 3.27 (0.26), residues: 358 sheet: -0.93 (0.52), residues: 102 loop : -1.10 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.012 0.002 PHE A 370 TYR 0.014 0.001 TYR A 150 ARG 0.003 0.000 ARG B 241 *********************** 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: 20 poor density : 72 time to evaluate : 0.627 Fit side-chains REVERT: B 63 ASP cc_start: 0.5913 (t0) cc_final: 0.5670 (t0) outliers start: 20 outliers final: 14 residues processed: 84 average time/residue: 0.1539 time to fit residues: 19.2654 Evaluate side-chains 79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 A residue 393 SER 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 Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.174229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138837 restraints weight = 12015.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138787 restraints weight = 11428.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139470 restraints weight = 11130.523| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7964 Z= 0.200 Angle : 0.545 6.616 11398 Z= 0.288 Chirality : 0.035 0.210 1434 Planarity : 0.003 0.033 1009 Dihedral : 23.218 176.944 2547 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.33 % Allowed : 22.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.33), residues: 699 helix: 3.30 (0.26), residues: 360 sheet: -0.99 (0.52), residues: 102 loop : -1.07 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.002 PHE A 319 TYR 0.016 0.002 TYR A 150 ARG 0.004 0.000 ARG B 241 *********************** 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 89 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.660 Fit side-chains REVERT: A 135 MET cc_start: 0.6401 (mtp) cc_final: 0.6170 (mtp) REVERT: B 192 ASN cc_start: 0.8003 (t0) cc_final: 0.7769 (t0) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.1350 time to fit residues: 17.1480 Evaluate side-chains 79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 392 LEU Chi-restraints excluded: chain A residue 393 SER 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 256 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.176561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139167 restraints weight = 11960.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141539 restraints weight = 10236.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141639 restraints weight = 7584.752| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7964 Z= 0.155 Angle : 0.506 6.330 11398 Z= 0.272 Chirality : 0.034 0.190 1434 Planarity : 0.003 0.031 1009 Dihedral : 23.135 177.211 2547 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.57 % Allowed : 22.60 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.33), residues: 699 helix: 3.50 (0.26), residues: 359 sheet: -0.96 (0.51), residues: 102 loop : -1.10 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.019 0.001 PHE A 319 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 241 *********************** 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 84 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.656 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.1183 time to fit residues: 14.9686 Evaluate side-chains 75 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 201 THR 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 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 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.176328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140516 restraints weight = 11881.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140759 restraints weight = 11903.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141332 restraints weight = 10843.620| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7964 Z= 0.158 Angle : 0.507 6.264 11398 Z= 0.271 Chirality : 0.034 0.185 1434 Planarity : 0.003 0.030 1009 Dihedral : 23.111 177.423 2547 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.81 % Allowed : 23.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.33), residues: 699 helix: 3.56 (0.26), residues: 359 sheet: -0.96 (0.51), residues: 102 loop : -1.12 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.001 PHE A 319 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 241 *********************** 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 83 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.624 Fit side-chains REVERT: A 327 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7660 (tm-30) outliers start: 20 outliers final: 17 residues processed: 78 average time/residue: 0.1326 time to fit residues: 16.6630 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 : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 201 THR 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 393 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 27 ASP 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 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 73 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.176613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138247 restraints weight = 12017.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140787 restraints weight = 9960.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141273 restraints weight = 7010.167| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7964 Z= 0.161 Angle : 0.505 6.206 11398 Z= 0.270 Chirality : 0.034 0.190 1434 Planarity : 0.003 0.030 1009 Dihedral : 23.102 177.342 2547 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.57 % Allowed : 24.04 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.33), residues: 699 helix: 3.58 (0.26), residues: 360 sheet: -0.92 (0.51), residues: 101 loop : -1.13 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.002 PHE A 319 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 241 *********************** 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: 19 poor density : 68 time to evaluate : 0.622 Fit side-chains REVERT: A 327 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7902 (tm-30) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.1332 time to fit residues: 16.6124 Evaluate side-chains 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 201 THR 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 393 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 27 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.178543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143086 restraints weight = 12000.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143351 restraints weight = 12042.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144051 restraints weight = 10070.448| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7964 Z= 0.151 Angle : 0.501 7.151 11398 Z= 0.268 Chirality : 0.033 0.199 1434 Planarity : 0.003 0.029 1009 Dihedral : 23.080 177.216 2547 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.85 % Allowed : 24.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.33), residues: 699 helix: 3.64 (0.26), residues: 362 sheet: -0.67 (0.50), residues: 108 loop : -1.20 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.002 0.001 HIS A 160 PHE 0.019 0.001 PHE A 319 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 241 *********************** 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 82 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.651 Fit side-chains REVERT: A 327 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7736 (tm-30) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.1269 time to fit residues: 15.8351 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 : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.175433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139713 restraints weight = 11961.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139929 restraints weight = 12074.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140545 restraints weight = 10221.834| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.003 0.028 7964 Z= 0.206 Angle : 0.542 6.802 11398 Z= 0.288 Chirality : 0.035 0.192 1434 Planarity : 0.003 0.029 1009 Dihedral : 23.135 177.502 2547 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.61 % Allowed : 24.28 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.33), residues: 699 helix: 3.53 (0.26), residues: 362 sheet: -0.77 (0.50), residues: 108 loop : -1.32 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.020 0.002 PHE A 319 TYR 0.016 0.002 TYR A 367 ARG 0.002 0.000 ARG B 241 ********************** 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 81 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.656 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 78 average time/residue: 0.1335 time to fit residues: 16.2194 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 : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 40.0000 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.177129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141490 restraints weight = 11943.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141585 restraints weight = 11925.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142305 restraints weight = 10225.812| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7964 Z= 0.169 Angle : 0.521 6.602 11398 Z= 0.278 Chirality : 0.034 0.201 1434 Planarity : 0.003 0.030 1009 Dihedral : 23.131 177.134 2547 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.61 % Allowed : 24.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.33), residues: 699 helix: 3.56 (0.26), residues: 362 sheet: -0.58 (0.50), residues: 110 loop : -1.32 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 PHE 0.020 0.002 PHE A 319 TYR 0.016 0.001 TYR A 367 ARG 0.003 0.000 ARG B 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.80 seconds wall clock time: 37 minutes 53.11 seconds (2273.11 seconds total)