Starting phenix.real_space_refine on Fri Sep 11 21:23:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l48_23157/09_2026/7l48_23157.map" } resolution = 3.9 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 144 5.49 5 S 37 5.16 5 C 6739 2.51 5 N 2052 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3074 Classifications: {'RNAv2': 144} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 16, 'rna3p': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3837 SG CYS A 475 13.590 59.792 45.199 1.00144.72 S ATOM 4048 SG CYS A 500 11.483 59.182 41.090 1.00168.30 S ATOM 364 SG CYS A 50 53.063 98.075 78.234 1.00132.99 S ATOM 502 SG CYS A 69 56.898 98.778 78.930 1.00109.77 S ATOM 527 SG CYS A 72 55.165 95.811 80.252 1.00111.13 S ATOM 8022 SG CYS B 475 60.243 58.550 15.167 1.00129.53 S ATOM 8043 SG CYS B 478 59.669 57.064 10.831 1.00129.65 S ATOM 4570 SG CYS B 50 29.666 39.470 31.268 1.00448.64 S Time building chain proxies: 2.26, per 1000 atoms: 0.20 Number of scatterers: 11488 At special positions: 0 Unit cell: (101.85, 119.7, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 144 15.00 O 2512 8.00 N 2052 7.00 C 6739 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: 0.84 Conformation dependent library (CDL) restraints added in 442.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 475 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 475 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 50 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 43.8% alpha, 9.3% beta 47 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.665A pdb=" N ASN A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.335A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.472A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.629A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.855A pdb=" N ARG A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.597A pdb=" N GLU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 382 through 414 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.857A pdb=" N MET A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 519 removed outlier: 4.673A pdb=" N ILE A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.720A pdb=" N ALA B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.242A pdb=" N LYS B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.831A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.807A pdb=" N ALA B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.585A pdb=" N LEU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.998A pdb=" N GLY B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 382 through 415 removed outlier: 3.954A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.572A pdb=" N ARG B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.743A pdb=" N ILE B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.215A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 251 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 253 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.931A pdb=" N ALA A 49 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 64 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 7.032A pdb=" N GLY A 323 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.649A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 5.507A pdb=" N THR B 418 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 321 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN B 420 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 462 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 500 365 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2651 1.34 - 1.46: 3594 1.46 - 1.58: 5439 1.58 - 1.71: 286 1.71 - 1.83: 51 Bond restraints: 12021 Sorted by residual: bond pdb=" CA SER B 51 " pdb=" CB SER B 51 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.59e-02 3.96e+03 2.17e+01 bond pdb=" N LYS A 383 " pdb=" CA LYS A 383 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N LEU A 194 " pdb=" CA LEU A 194 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.94e+00 ... (remaining 12016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 15871 2.23 - 4.46: 868 4.46 - 6.69: 109 6.69 - 8.92: 20 8.92 - 11.15: 7 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N GLU B 390 " pdb=" CA GLU B 390 " pdb=" CB GLU B 390 " ideal model delta sigma weight residual 110.12 118.78 -8.66 1.47e+00 4.63e-01 3.47e+01 angle pdb=" C PHE A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N GLN B 88 " pdb=" CA GLN B 88 " pdb=" CB GLN B 88 " ideal model delta sigma weight residual 110.13 118.64 -8.51 1.48e+00 4.57e-01 3.31e+01 angle pdb=" C PRO B 219 " pdb=" N PHE B 220 " pdb=" CA PHE B 220 " ideal model delta sigma weight residual 122.20 130.82 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 6605 35.59 - 71.17: 381 71.17 - 106.76: 13 106.76 - 142.34: 0 142.34 - 177.92: 1 Dihedral angle restraints: 7000 sinusoidal: 3933 harmonic: 3067 Sorted by residual: dihedral pdb=" C4' U E 70 " pdb=" C3' U E 70 " pdb=" C2' U E 70 " pdb=" C1' U E 70 " ideal model delta sinusoidal sigma weight residual 36.34 -37.66 74.00 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' A E 192 " pdb=" C3' A E 192 " pdb=" C2' A E 192 " pdb=" C1' A E 192 " ideal model delta sinusoidal sigma weight residual 36.34 -37.13 73.47 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' G E 190 " pdb=" C3' G E 190 " pdb=" C2' G E 190 " pdb=" C1' G E 190 " ideal model delta sinusoidal sigma weight residual 36.35 -36.86 73.20 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1583 0.093 - 0.185: 148 0.185 - 0.278: 192 0.278 - 0.370: 18 0.370 - 0.463: 3 Chirality restraints: 1944 Sorted by residual: chirality pdb=" P G E 61 " pdb=" OP1 G E 61 " pdb=" OP2 G E 61 " pdb=" O5' G E 61 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" P A E 191 " pdb=" OP1 A E 191 " pdb=" OP2 A E 191 " pdb=" O5' A E 191 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1941 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 52 " 0.025 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C LYS B 52 " -0.090 2.00e-02 2.50e+03 pdb=" O LYS B 52 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS B 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 48 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLU B 48 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU B 48 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 84 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 84 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 84 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2561 2.79 - 3.32: 10342 3.32 - 3.85: 21243 3.85 - 4.37: 24108 4.37 - 4.90: 36428 Nonbonded interactions: 94682 Sorted by model distance: nonbonded pdb=" OG SER B 51 " pdb=" CD ARG B 66 " model vdw 2.263 3.440 nonbonded pdb=" O ASN A 133 " pdb=" OG SER A 136 " model vdw 2.273 3.040 nonbonded pdb=" N6 A E 100 " pdb=" O2 C E 123 " model vdw 2.283 3.120 nonbonded pdb=" OG SER A 476 " pdb=" ND2 ASN A 512 " model vdw 2.298 3.120 nonbonded pdb=" C SER B 51 " pdb=" OG SER B 51 " model vdw 2.302 2.616 ... (remaining 94677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.160 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.008 0.692 12030 Z= 0.335 Angle : 1.075 11.153 16878 Z= 0.554 Chirality : 0.095 0.463 1944 Planarity : 0.006 0.061 1620 Dihedral : 18.608 177.925 5010 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.21 % Cbeta Deviations : 0.20 % 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 are not related in a simple way. whole: -3.57 (0.21), residues: 1037 helix: -1.48 (0.20), residues: 441 sheet: -2.30 (0.40), residues: 132 loop : -3.27 (0.22), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 363 TYR 0.032 0.002 TYR B 121 PHE 0.060 0.003 PHE A 354 TRP 0.035 0.003 TRP B 223 HIS 0.028 0.003 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.26 (12021) covalent geometry : angle 1.07079 / 0.55 (16875) hydrogen bonds : bond 0.14342 / 9.59 ( 479) hydrogen bonds : angle 6.55054 / 4.88 ( 1281) metal coordination : bond 0.23892 / 15.57 ( 9) metal coordination : angle 6.88555 / 4.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8106 (t80) cc_final: 0.7831 (t80) REVERT: A 421 MET cc_start: 0.7801 (tmm) cc_final: 0.7521 (tmm) REVERT: A 510 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30) REVERT: B 353 HIS cc_start: 0.8389 (t-90) cc_final: 0.8095 (t-170) REVERT: B 358 MET cc_start: 0.8598 (tpt) cc_final: 0.8078 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1113 time to fit residues: 14.1366 Evaluate side-chains 53 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN A 519 ASN B 32 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.069880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051209 restraints weight = 62498.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052526 restraints weight = 34136.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053221 restraints weight = 23768.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053692 restraints weight = 19504.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053912 restraints weight = 17337.763| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12030 Z= 0.297 Angle : 1.013 14.113 16878 Z= 0.454 Chirality : 0.070 0.725 1944 Planarity : 0.005 0.042 1620 Dihedral : 16.539 165.620 2858 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 1.78 % Allowed : 11.69 % Favored : 86.53 % 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 are not related in a simple way. whole: -2.37 (0.24), residues: 1037 helix: -0.18 (0.23), residues: 463 sheet: -2.24 (0.41), residues: 140 loop : -2.92 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 13 TYR 0.023 0.002 TYR A 82 PHE 0.025 0.002 PHE B 220 TRP 0.014 0.002 TRP B 223 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.30 (12021) covalent geometry : angle 1.01224 / 0.45 (16875) hydrogen bonds : bond 0.05497 / 3.88 ( 479) hydrogen bonds : angle 4.91202 / 3.59 ( 1281) metal coordination : bond 0.01451 / 0.72 ( 9) metal coordination : angle 3.24834 / 3.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8579 (ttt) cc_final: 0.8307 (tpp) REVERT: A 357 LYS cc_start: 0.9156 (pptt) cc_final: 0.8715 (pptt) REVERT: A 510 ASP cc_start: 0.8693 (m-30) cc_final: 0.8413 (m-30) REVERT: A 515 LEU cc_start: 0.9011 (tp) cc_final: 0.8614 (mt) REVERT: B 353 HIS cc_start: 0.8809 (t-90) cc_final: 0.8369 (t-170) REVERT: B 358 MET cc_start: 0.8798 (tpt) cc_final: 0.8594 (tpp) outliers start: 16 outliers final: 9 residues processed: 78 average time/residue: 0.1191 time to fit residues: 13.3450 Evaluate side-chains 58 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS A 512 ASN A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.071744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053186 restraints weight = 62328.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.054582 restraints weight = 33329.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.055406 restraints weight = 22700.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.055865 restraints weight = 18075.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056091 restraints weight = 15868.228| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12030 Z= 0.148 Angle : 0.794 10.229 16878 Z= 0.356 Chirality : 0.059 0.485 1944 Planarity : 0.004 0.037 1620 Dihedral : 16.180 168.264 2858 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.67 % Allowed : 13.92 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.25), residues: 1037 helix: 0.55 (0.24), residues: 459 sheet: -2.08 (0.42), residues: 142 loop : -2.70 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.019 0.002 TYR A 82 PHE 0.022 0.001 PHE A 341 TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (12021) covalent geometry : angle 0.79333 / 0.36 (16875) hydrogen bonds : bond 0.04751 / 3.25 ( 479) hydrogen bonds : angle 4.34343 / 3.14 ( 1281) metal coordination : bond 0.00531 / 0.27 ( 9) metal coordination : angle 1.56796 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.9131 (pptt) cc_final: 0.8837 (pptt) REVERT: A 510 ASP cc_start: 0.8386 (m-30) cc_final: 0.8105 (m-30) REVERT: B 353 HIS cc_start: 0.8661 (t-90) cc_final: 0.8428 (t-170) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.0923 time to fit residues: 10.3400 Evaluate side-chains 58 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.071668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052233 restraints weight = 63452.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053650 restraints weight = 33178.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.054468 restraints weight = 22489.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054975 restraints weight = 18030.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055208 restraints weight = 15892.780| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12030 Z= 0.161 Angle : 0.786 9.667 16878 Z= 0.350 Chirality : 0.057 0.417 1944 Planarity : 0.004 0.037 1620 Dihedral : 15.914 167.716 2858 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.00 % Allowed : 16.70 % Favored : 81.29 % 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 are not related in a simple way. whole: -1.34 (0.26), residues: 1037 helix: 0.93 (0.24), residues: 458 sheet: -1.83 (0.43), residues: 142 loop : -2.62 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.022 0.002 TYR A 82 PHE 0.017 0.001 PHE A 341 TRP 0.009 0.001 TRP B 223 HIS 0.002 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (12021) covalent geometry : angle 0.78537 / 0.35 (16875) hydrogen bonds : bond 0.04909 / 3.42 ( 479) hydrogen bonds : angle 4.18923 / 3.01 ( 1281) metal coordination : bond 0.00914 / 0.45 ( 9) metal coordination : angle 1.75953 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8366 (ttt) cc_final: 0.7971 (tpp) REVERT: A 346 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6089 (mp) REVERT: A 354 PHE cc_start: 0.8715 (t80) cc_final: 0.8319 (t80) REVERT: A 510 ASP cc_start: 0.8387 (m-30) cc_final: 0.8122 (m-30) REVERT: B 353 HIS cc_start: 0.8911 (t-90) cc_final: 0.8658 (t-170) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.0932 time to fit residues: 10.2757 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 169 ASN A 210 HIS A 338 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.068343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049145 restraints weight = 64564.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050514 restraints weight = 33570.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051284 restraints weight = 22860.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051720 restraints weight = 18428.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051857 restraints weight = 16390.525| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12030 Z= 0.268 Angle : 0.897 9.675 16878 Z= 0.403 Chirality : 0.060 0.470 1944 Planarity : 0.005 0.037 1620 Dihedral : 16.045 165.437 2858 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.78 % Allowed : 17.71 % Favored : 79.51 % 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 are not related in a simple way. whole: -1.46 (0.26), residues: 1037 helix: 0.76 (0.24), residues: 460 sheet: -1.89 (0.43), residues: 143 loop : -2.62 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 16 TYR 0.027 0.002 TYR A 82 PHE 0.018 0.002 PHE B 495 TRP 0.011 0.001 TRP A 223 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.27 (12021) covalent geometry : angle 0.89623 / 0.40 (16875) hydrogen bonds : bond 0.05891 / 4.10 ( 479) hydrogen bonds : angle 4.51740 / 3.22 ( 1281) metal coordination : bond 0.01880 / 0.93 ( 9) metal coordination : angle 2.29573 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8456 (ttt) cc_final: 0.7849 (tpp) REVERT: A 194 LEU cc_start: 0.9416 (mp) cc_final: 0.9175 (mp) REVERT: A 346 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6411 (mp) REVERT: A 510 ASP cc_start: 0.8594 (m-30) cc_final: 0.8204 (m-30) REVERT: B 292 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7296 (ppt90) REVERT: B 353 HIS cc_start: 0.9021 (t-90) cc_final: 0.8618 (t-170) outliers start: 25 outliers final: 16 residues processed: 70 average time/residue: 0.1075 time to fit residues: 11.3134 Evaluate side-chains 63 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.070509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051180 restraints weight = 64181.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052598 restraints weight = 33214.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053418 restraints weight = 22575.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.053879 restraints weight = 18063.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054097 restraints weight = 15979.952| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12030 Z= 0.158 Angle : 0.794 9.997 16878 Z= 0.354 Chirality : 0.057 0.396 1944 Planarity : 0.004 0.036 1620 Dihedral : 15.757 167.321 2858 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.12 % Allowed : 18.82 % Favored : 79.06 % 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 are not related in a simple way. whole: -1.15 (0.26), residues: 1037 helix: 1.07 (0.24), residues: 462 sheet: -1.79 (0.44), residues: 142 loop : -2.50 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.024 0.002 TYR A 82 PHE 0.012 0.001 PHE A 341 TRP 0.010 0.001 TRP B 443 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (12021) covalent geometry : angle 0.79356 / 0.35 (16875) hydrogen bonds : bond 0.04931 / 3.43 ( 479) hydrogen bonds : angle 4.22089 / 3.01 ( 1281) metal coordination : bond 0.00892 / 0.43 ( 9) metal coordination : angle 1.53838 / 1.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8860 (t80) cc_final: 0.8303 (t80) REVERT: A 178 MET cc_start: 0.8376 (ttt) cc_final: 0.7912 (tpp) REVERT: A 194 LEU cc_start: 0.9392 (mp) cc_final: 0.9134 (mp) REVERT: A 354 PHE cc_start: 0.8755 (t80) cc_final: 0.8259 (t80) REVERT: A 510 ASP cc_start: 0.8374 (m-30) cc_final: 0.8078 (m-30) REVERT: B 353 HIS cc_start: 0.8911 (t-90) cc_final: 0.8527 (t-170) REVERT: B 358 MET cc_start: 0.8801 (tpp) cc_final: 0.8471 (tpp) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.0959 time to fit residues: 10.5108 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.071200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051835 restraints weight = 64194.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053293 restraints weight = 32895.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054116 restraints weight = 22144.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054495 restraints weight = 17731.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054768 restraints weight = 16003.066| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12030 Z= 0.142 Angle : 0.782 14.616 16878 Z= 0.346 Chirality : 0.056 0.402 1944 Planarity : 0.004 0.036 1620 Dihedral : 15.639 166.954 2858 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.00 % Allowed : 19.71 % Favored : 78.29 % 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 are not related in a simple way. whole: -0.95 (0.27), residues: 1037 helix: 1.23 (0.24), residues: 461 sheet: -1.75 (0.44), residues: 143 loop : -2.37 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.022 0.001 TYR A 82 PHE 0.010 0.001 PHE A 341 TRP 0.009 0.001 TRP B 223 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12021) covalent geometry : angle 0.78194 / 0.35 (16875) hydrogen bonds : bond 0.04805 / 3.36 ( 479) hydrogen bonds : angle 4.21505 / 3.03 ( 1281) metal coordination : bond 0.00743 / 0.36 ( 9) metal coordination : angle 1.40868 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8913 (t80) cc_final: 0.8350 (t80) REVERT: A 178 MET cc_start: 0.8417 (ttt) cc_final: 0.8080 (tpp) REVERT: A 194 LEU cc_start: 0.9401 (mp) cc_final: 0.9137 (mp) REVERT: A 346 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6371 (mp) REVERT: A 510 ASP cc_start: 0.8316 (m-30) cc_final: 0.8022 (m-30) REVERT: B 358 MET cc_start: 0.8871 (tpp) cc_final: 0.8650 (tpp) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.0833 time to fit residues: 9.6537 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.071598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052637 restraints weight = 63677.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054056 restraints weight = 33176.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054915 restraints weight = 22481.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055364 restraints weight = 17974.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.055567 restraints weight = 15833.382| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12030 Z= 0.143 Angle : 0.781 12.745 16878 Z= 0.346 Chirality : 0.056 0.400 1944 Planarity : 0.004 0.037 1620 Dihedral : 15.609 166.634 2858 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.45 % Allowed : 19.60 % Favored : 77.95 % 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 are not related in a simple way. whole: -0.83 (0.27), residues: 1037 helix: 1.31 (0.24), residues: 461 sheet: -1.63 (0.44), residues: 143 loop : -2.30 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.022 0.001 TYR A 82 PHE 0.014 0.001 PHE B 125 TRP 0.009 0.001 TRP B 223 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12021) covalent geometry : angle 0.78062 / 0.35 (16875) hydrogen bonds : bond 0.04774 / 3.32 ( 479) hydrogen bonds : angle 4.12029 / 2.98 ( 1281) metal coordination : bond 0.00816 / 0.39 ( 9) metal coordination : angle 1.34532 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: A 121 TYR cc_start: 0.8878 (t80) cc_final: 0.8305 (t80) REVERT: A 178 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: A 194 LEU cc_start: 0.9402 (mp) cc_final: 0.9137 (mp) REVERT: A 346 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6319 (mp) REVERT: A 510 ASP cc_start: 0.8325 (m-30) cc_final: 0.8061 (m-30) REVERT: B 78 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7909 (t70) REVERT: B 358 MET cc_start: 0.8901 (tpp) cc_final: 0.8689 (tpp) outliers start: 22 outliers final: 14 residues processed: 71 average time/residue: 0.0846 time to fit residues: 9.3535 Evaluate side-chains 69 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.070374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052753 restraints weight = 63864.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053777 restraints weight = 36604.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053959 restraints weight = 23247.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054109 restraints weight = 19872.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054115 restraints weight = 18576.455| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12030 Z= 0.185 Angle : 0.806 13.378 16878 Z= 0.361 Chirality : 0.056 0.398 1944 Planarity : 0.004 0.038 1620 Dihedral : 15.735 165.933 2858 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.23 % Allowed : 20.38 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.27), residues: 1037 helix: 1.27 (0.24), residues: 458 sheet: -1.59 (0.44), residues: 142 loop : -2.24 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 259 TYR 0.048 0.002 TYR A 140 PHE 0.022 0.002 PHE A 214 TRP 0.009 0.001 TRP A 223 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (12021) covalent geometry : angle 0.80600 / 0.36 (16875) hydrogen bonds : bond 0.05094 / 3.54 ( 479) hydrogen bonds : angle 4.25953 / 3.06 ( 1281) metal coordination : bond 0.01188 / 0.57 ( 9) metal coordination : angle 1.51468 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6526 (m-10) REVERT: A 121 TYR cc_start: 0.8855 (t80) cc_final: 0.8337 (t80) REVERT: A 178 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8041 (tpp) REVERT: A 194 LEU cc_start: 0.9393 (mp) cc_final: 0.9185 (mp) REVERT: A 346 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6393 (mp) REVERT: A 510 ASP cc_start: 0.8354 (m-30) cc_final: 0.8077 (m-30) REVERT: B 78 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7601 (t70) REVERT: B 358 MET cc_start: 0.8882 (tpp) cc_final: 0.8678 (tpp) REVERT: B 421 MET cc_start: 0.7168 (tmm) cc_final: 0.6960 (tmm) outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.0962 time to fit residues: 9.8542 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.053392 restraints weight = 63842.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054561 restraints weight = 37341.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054599 restraints weight = 23183.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054782 restraints weight = 21679.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054977 restraints weight = 19075.904| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12030 Z= 0.154 Angle : 0.787 13.858 16878 Z= 0.351 Chirality : 0.056 0.386 1944 Planarity : 0.004 0.037 1620 Dihedral : 15.674 166.495 2858 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.34 % Allowed : 20.49 % Favored : 77.17 % 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 are not related in a simple way. whole: -0.82 (0.27), residues: 1037 helix: 1.28 (0.24), residues: 456 sheet: -1.57 (0.44), residues: 139 loop : -2.21 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.041 0.002 TYR A 140 PHE 0.013 0.001 PHE B 125 TRP 0.008 0.001 TRP B 223 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12021) covalent geometry : angle 0.78703 / 0.35 (16875) hydrogen bonds : bond 0.04789 / 3.31 ( 479) hydrogen bonds : angle 4.19630 / 3.01 ( 1281) metal coordination : bond 0.00827 / 0.40 ( 9) metal coordination : angle 1.29565 / 1.12 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 121 TYR cc_start: 0.8874 (t80) cc_final: 0.8345 (t80) REVERT: A 178 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: A 194 LEU cc_start: 0.9392 (mp) cc_final: 0.9137 (mp) REVERT: A 346 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6412 (mp) REVERT: A 510 ASP cc_start: 0.8382 (m-30) cc_final: 0.8118 (m-30) REVERT: B 78 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7643 (t70) REVERT: B 358 MET cc_start: 0.8884 (tpp) cc_final: 0.8668 (tpp) REVERT: B 421 MET cc_start: 0.7182 (tmm) cc_final: 0.6981 (tmm) outliers start: 21 outliers final: 15 residues processed: 73 average time/residue: 0.0940 time to fit residues: 10.3677 Evaluate side-chains 72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 0.0060 chunk 84 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 83 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.072609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.055112 restraints weight = 63980.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.055374 restraints weight = 35519.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055824 restraints weight = 24607.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055866 restraints weight = 20377.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.055869 restraints weight = 19885.583| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12030 Z= 0.124 Angle : 0.769 13.334 16878 Z= 0.344 Chirality : 0.055 0.427 1944 Planarity : 0.004 0.039 1620 Dihedral : 15.486 166.617 2858 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.78 % Allowed : 20.82 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.27), residues: 1037 helix: 1.35 (0.25), residues: 457 sheet: -1.76 (0.43), residues: 144 loop : -2.18 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 363 TYR 0.038 0.001 TYR A 140 PHE 0.014 0.001 PHE B 125 TRP 0.010 0.001 TRP B 223 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (12021) covalent geometry : angle 0.76862 / 0.34 (16875) hydrogen bonds : bond 0.04540 / 3.11 ( 479) hydrogen bonds : angle 4.08719 / 2.92 ( 1281) metal coordination : bond 0.00482 / 0.23 ( 9) metal coordination : angle 1.14178 / 1.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.23 seconds wall clock time: 32 minutes 52.22 seconds (1972.22 seconds total)