Starting phenix.real_space_refine on Sat May 2 13:31:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrl_73370/05_2026/9yrl_73370.map" } resolution = 2.9 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= 0.011 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: 8 Type Number sf(0) Gaussians Zn 5 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 3561 2.51 5 N 989 2.21 5 O 1164 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5808 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4086 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 bond proxies already assigned to first conformer: 4182 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 680 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 29} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'EIF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 50.778 76.370 70.055 1.00 53.46 S ATOM 546 SG CYS A 77 50.123 74.396 73.283 1.00 45.86 S ATOM 651 SG CYS A 90 51.965 77.703 73.424 1.00 58.85 S ATOM 854 SG CYS A 117 54.768 96.439 67.492 1.00 99.85 S ATOM 874 SG CYS A 120 51.666 97.623 69.149 1.00 94.16 S ATOM 935 SG CYS A 128 52.007 97.793 65.359 1.00111.32 S ATOM 947 SG CYS A 130 53.808 100.292 67.524 1.00120.94 S ATOM 2578 SG CYS B 207 68.642 60.320 48.534 1.00 51.68 S ATOM 2598 SG CYS B 210 69.646 59.270 45.969 1.00 62.24 S ATOM 2719 SG CYS B 226 68.589 56.888 48.133 1.00 45.60 S ATOM 3019 SG CYS B 261 52.168 29.167 55.441 1.00 72.40 S ATOM 3149 SG CYS B 279 51.680 32.793 53.949 1.00 57.00 S ATOM 4539 SG CYS B 452 82.274 22.861 10.711 1.00175.36 S ATOM 4653 SG CYS B 477 82.748 21.743 14.453 1.00165.94 S ATOM 4695 SG CYS B 484 82.697 25.506 13.439 1.00167.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 95 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS B 95 " occ=0.47 Time building chain proxies: 2.48, per 1000 atoms: 0.43 Number of scatterers: 5808 At special positions: 0 Unit cell: (99.7332, 111.53, 105.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 S 52 16.00 P 35 15.00 Mg 1 11.99 F 1 9.00 O 1164 8.00 N 989 7.00 C 3561 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 558.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 477 " Number of angles added : 17 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1202 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 30.8% alpha, 17.3% beta 17 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.309A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 143 through 148 removed outlier: 5.066A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.701A pdb=" N MET B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 158 through 175 removed outlier: 4.017A pdb=" N ILE B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.117A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.508A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.509A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.666A pdb=" N ALA B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 484 through 505 Processing helix chain 'B' and resid 515 through 523 removed outlier: 4.022A pdb=" N TRP B 520 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.656A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.712A pdb=" N GLU B 364 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 328 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B 383 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 330 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TRP B 385 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 332 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.368A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 169 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1567 1.33 - 1.45: 1350 1.45 - 1.57: 2977 1.57 - 1.69: 67 1.69 - 1.81: 68 Bond restraints: 6029 Sorted by residual: bond pdb=" O3 EIF C 101 " pdb=" P EIF C 101 " ideal model delta sigma weight residual 1.670 1.519 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL B 341 " pdb=" CA VAL B 341 " ideal model delta sigma weight residual 1.456 1.496 -0.041 8.60e-03 1.35e+04 2.22e+01 bond pdb=" N EIF C 101 " pdb=" C6 EIF C 101 " ideal model delta sigma weight residual 1.440 1.370 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O4 EIF C 101 " pdb=" P EIF C 101 " ideal model delta sigma weight residual 1.463 1.517 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C7 EIF C 101 " pdb=" C8 EIF C 101 " ideal model delta sigma weight residual 1.430 1.376 0.054 2.00e-02 2.50e+03 7.32e+00 ... (remaining 6024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 8260 2.63 - 5.25: 90 5.25 - 7.88: 6 7.88 - 10.51: 0 10.51 - 13.14: 3 Bond angle restraints: 8359 Sorted by residual: angle pdb=" O3 EIF C 101 " pdb=" P EIF C 101 " pdb=" O4 EIF C 101 " ideal model delta sigma weight residual 128.40 115.26 13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA VAL B 341 " pdb=" C VAL B 341 " pdb=" O VAL B 341 " ideal model delta sigma weight residual 120.88 118.21 2.67 6.80e-01 2.16e+00 1.54e+01 angle pdb=" CA VAL B 341 " pdb=" C VAL B 341 " pdb=" N PRO B 342 " ideal model delta sigma weight residual 118.12 121.27 -3.15 8.10e-01 1.52e+00 1.51e+01 angle pdb=" O1 EIF C 101 " pdb=" P EIF C 101 " pdb=" O4 EIF C 101 " ideal model delta sigma weight residual 117.72 106.61 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O EIF C 101 " pdb=" C2 EIF C 101 " pdb=" C3 EIF C 101 " ideal model delta sigma weight residual 105.13 115.79 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 8354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3314 17.63 - 35.26: 183 35.26 - 52.90: 45 52.90 - 70.53: 29 70.53 - 88.16: 13 Dihedral angle restraints: 3584 sinusoidal: 1711 harmonic: 1873 Sorted by residual: dihedral pdb=" CA CYS B 356 " pdb=" C CYS B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 133 " pdb=" C PHE B 133 " pdb=" N SER B 134 " pdb=" CA SER B 134 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA VAL B 91 " pdb=" C VAL B 91 " pdb=" N GLU B 92 " pdb=" CA GLU B 92 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 862 0.081 - 0.161: 83 0.161 - 0.242: 1 0.242 - 0.323: 0 0.323 - 0.403: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" C2 EIF C 101 " pdb=" O EIF C 101 " pdb=" C1 EIF C 101 " pdb=" C3 EIF C 101 " both_signs ideal model delta sigma weight residual False -2.89 -2.49 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA VAL B 341 " pdb=" N VAL B 341 " pdb=" C VAL B 341 " pdb=" CB VAL B 341 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" C5 EIF C 101 " pdb=" N EIF C 101 " pdb=" C1 EIF C 101 " pdb=" O5 EIF C 101 " both_signs ideal model delta sigma weight residual False -2.55 -2.39 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 944 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BHIS B 95 " 0.027 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C BHIS B 95 " -0.095 2.00e-02 2.50e+03 pdb=" O BHIS B 95 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA B 96 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 488 " -0.012 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ALA B 488 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 488 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 489 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 20 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.19e+00 pdb=" C PRO B 20 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 20 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 21 " -0.010 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 34 2.59 - 3.17: 4599 3.17 - 3.75: 9250 3.75 - 4.32: 13226 4.32 - 4.90: 20892 Nonbonded interactions: 48001 Sorted by model distance: nonbonded pdb=" O ASN B 478 " pdb=" OD1 ASN B 478 " model vdw 2.018 3.040 nonbonded pdb=" OD1 ASP B 324 " pdb=" OH TYR B 511 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR B 472 " pdb=" OH TYR B 491 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.326 2.170 nonbonded pdb=" O TYR B 370 " pdb=" OG SER B 374 " model vdw 2.337 3.040 ... (remaining 47996 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.240 Find NCS groups from input model: 0.020 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:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.006 0.192 6050 Z= 0.289 Angle : 0.860 32.279 8376 Z= 0.430 Chirality : 0.046 0.403 947 Planarity : 0.006 0.055 940 Dihedral : 14.106 88.162 2382 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -0.29 (0.33), residues: 639 helix: 0.05 (0.42), residues: 146 sheet: -1.12 (0.51), residues: 87 loop : 0.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.011 0.002 TYR B 420 PHE 0.021 0.002 PHE B 133 TRP 0.016 0.002 TRP B 227 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 6029) covalent geometry : angle 0.73571 ( 8359) hydrogen bonds : bond 0.14439 ( 201) hydrogen bonds : angle 6.22886 ( 530) metal coordination : bond 0.04461 ( 20) metal coordination : angle 9.89633 ( 17) Misc. bond : bond 0.03967 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.213 Fit side-chains REVERT: A 5 THR cc_start: 0.8165 (m) cc_final: 0.7706 (m) REVERT: A 53 GLN cc_start: 0.8409 (mt0) cc_final: 0.8139 (mt0) REVERT: A 101 THR cc_start: 0.8528 (t) cc_final: 0.7939 (m) REVERT: B 49 MET cc_start: 0.7994 (ttp) cc_final: 0.7778 (ttp) REVERT: B 61 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8078 (mtpp) REVERT: B 76 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7743 (ptm160) REVERT: B 77 GLU cc_start: 0.7115 (mp0) cc_final: 0.6794 (mp0) REVERT: B 92 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 126 ASP cc_start: 0.7854 (t70) cc_final: 0.7649 (m-30) REVERT: B 154 TYR cc_start: 0.8261 (m-80) cc_final: 0.7848 (m-80) REVERT: B 175 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8102 (ttmm) REVERT: B 304 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7241 (mmtt) REVERT: B 313 GLN cc_start: 0.7693 (tt0) cc_final: 0.7464 (tt0) REVERT: B 318 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7484 (ttpp) REVERT: B 339 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7251 (mtmm) REVERT: B 347 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6304 (mm-30) REVERT: B 349 LYS cc_start: 0.7269 (mttt) cc_final: 0.6783 (mttt) REVERT: B 352 ASP cc_start: 0.5486 (t0) cc_final: 0.4883 (t70) REVERT: B 492 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6867 (mtm110) REVERT: B 511 TYR cc_start: 0.7593 (p90) cc_final: 0.7070 (p90) outliers start: 0 outliers final: 1 residues processed: 154 average time/residue: 0.5925 time to fit residues: 94.9754 Evaluate side-chains 127 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 330 HIS B 438 ASN B 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110655 restraints weight = 12523.211| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.28 r_work: 0.3272 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6050 Z= 0.163 Angle : 0.592 9.951 8376 Z= 0.299 Chirality : 0.042 0.148 947 Planarity : 0.005 0.043 940 Dihedral : 13.550 80.470 1240 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 13.38 % Favored : 84.99 % 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: 0.02 (0.34), residues: 639 helix: 0.61 (0.44), residues: 145 sheet: -1.08 (0.53), residues: 81 loop : 0.13 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 400 TYR 0.021 0.002 TYR B 491 PHE 0.018 0.002 PHE B 133 TRP 0.016 0.002 TRP B 520 HIS 0.006 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6029) covalent geometry : angle 0.56133 ( 8359) hydrogen bonds : bond 0.04234 ( 201) hydrogen bonds : angle 4.46751 ( 530) metal coordination : bond 0.01432 ( 20) metal coordination : angle 4.24199 ( 17) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.222 Fit side-chains REVERT: A 5 THR cc_start: 0.8257 (m) cc_final: 0.7833 (m) REVERT: A 66 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 101 THR cc_start: 0.8531 (t) cc_final: 0.8019 (m) REVERT: B 49 MET cc_start: 0.7988 (ttp) cc_final: 0.7692 (ttp) REVERT: B 61 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8123 (mtpp) REVERT: B 77 GLU cc_start: 0.7451 (mp0) cc_final: 0.7222 (mp0) REVERT: B 92 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 154 TYR cc_start: 0.8282 (m-80) cc_final: 0.7868 (m-80) REVERT: B 231 ILE cc_start: 0.8529 (mm) cc_final: 0.8185 (tp) REVERT: B 349 LYS cc_start: 0.8114 (mttt) cc_final: 0.7843 (mtmm) REVERT: B 352 ASP cc_start: 0.6736 (t0) cc_final: 0.6137 (t0) REVERT: B 492 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7465 (mtm110) REVERT: B 511 TYR cc_start: 0.7892 (p90) cc_final: 0.7643 (p90) REVERT: B 520 TRP cc_start: 0.8060 (m100) cc_final: 0.7854 (m-90) outliers start: 9 outliers final: 3 residues processed: 135 average time/residue: 0.6065 time to fit residues: 85.2910 Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 80 HIS B 354 GLN ** B 478 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 = 0.3833 r_free = 0.3833 target = 0.140803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111713 restraints weight = 8569.974| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.81 r_work: 0.3309 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6050 Z= 0.191 Angle : 0.596 10.046 8376 Z= 0.298 Chirality : 0.042 0.147 947 Planarity : 0.004 0.044 940 Dihedral : 13.277 73.755 1238 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.53 % Allowed : 15.01 % Favored : 82.46 % 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: 0.11 (0.34), residues: 639 helix: 0.81 (0.44), residues: 146 sheet: -0.93 (0.53), residues: 81 loop : 0.11 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 400 TYR 0.020 0.002 TYR B 420 PHE 0.023 0.002 PHE B 350 TRP 0.016 0.002 TRP B 520 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6029) covalent geometry : angle 0.56438 ( 8359) hydrogen bonds : bond 0.04277 ( 201) hydrogen bonds : angle 4.29768 ( 530) metal coordination : bond 0.01596 ( 20) metal coordination : angle 4.31912 ( 17) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8299 (m) cc_final: 0.7880 (m) REVERT: A 58 THR cc_start: 0.8262 (t) cc_final: 0.8060 (p) REVERT: B 48 ASP cc_start: 0.7908 (t0) cc_final: 0.7645 (t0) REVERT: B 49 MET cc_start: 0.7896 (ttp) cc_final: 0.7621 (ttp) REVERT: B 57 MET cc_start: 0.8545 (mmt) cc_final: 0.8338 (mmm) REVERT: B 61 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8051 (mtpp) REVERT: B 154 TYR cc_start: 0.8281 (m-80) cc_final: 0.7908 (m-80) REVERT: B 169 MET cc_start: 0.8432 (ttp) cc_final: 0.8138 (OUTLIER) REVERT: B 318 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8078 (ttpp) REVERT: B 324 ASP cc_start: 0.7451 (m-30) cc_final: 0.7034 (m-30) REVERT: B 329 LEU cc_start: 0.8069 (tt) cc_final: 0.7756 (tp) REVERT: B 400 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7984 (mtp180) REVERT: B 492 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7486 (mtm110) REVERT: B 520 TRP cc_start: 0.8153 (m100) cc_final: 0.7897 (m-90) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 0.5935 time to fit residues: 79.1657 Evaluate side-chains 121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 0.0070 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 overall best weight: 0.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 313 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111250 restraints weight = 16945.876| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.70 r_work: 0.3261 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6050 Z= 0.111 Angle : 0.561 10.345 8376 Z= 0.283 Chirality : 0.042 0.367 947 Planarity : 0.004 0.043 940 Dihedral : 13.179 73.791 1238 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.81 % Allowed : 17.00 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.34), residues: 639 helix: 1.13 (0.45), residues: 144 sheet: -1.05 (0.52), residues: 81 loop : 0.20 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.017 0.001 TYR B 447 PHE 0.024 0.001 PHE B 444 TRP 0.014 0.001 TRP B 385 HIS 0.022 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6029) covalent geometry : angle 0.53915 ( 8359) hydrogen bonds : bond 0.03551 ( 201) hydrogen bonds : angle 4.07211 ( 530) metal coordination : bond 0.00938 ( 20) metal coordination : angle 3.44984 ( 17) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8234 (m) cc_final: 0.7835 (m) REVERT: A 58 THR cc_start: 0.8221 (t) cc_final: 0.8014 (p) REVERT: A 66 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 103 CYS cc_start: 0.8267 (m) cc_final: 0.8008 (m) REVERT: A 122 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8382 (mmm) REVERT: B 48 ASP cc_start: 0.7819 (t0) cc_final: 0.7569 (t0) REVERT: B 49 MET cc_start: 0.7759 (ttp) cc_final: 0.7519 (ttp) REVERT: B 57 MET cc_start: 0.8516 (mmt) cc_final: 0.8289 (mmm) REVERT: B 61 LYS cc_start: 0.8237 (mtpt) cc_final: 0.8002 (mtpp) REVERT: B 126 ASP cc_start: 0.7710 (m-30) cc_final: 0.7445 (m-30) REVERT: B 154 TYR cc_start: 0.8154 (m-80) cc_final: 0.7848 (m-80) REVERT: B 169 MET cc_start: 0.8334 (ttp) cc_final: 0.8030 (OUTLIER) REVERT: B 318 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8117 (tttp) REVERT: B 324 ASP cc_start: 0.7416 (m-30) cc_final: 0.6982 (m-30) REVERT: B 339 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7734 (mtpm) REVERT: B 352 ASP cc_start: 0.6311 (t0) cc_final: 0.5577 (t0) REVERT: B 400 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7923 (mtp180) REVERT: B 492 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7332 (mtm110) REVERT: B 520 TRP cc_start: 0.8085 (m100) cc_final: 0.7860 (m-90) outliers start: 10 outliers final: 4 residues processed: 125 average time/residue: 0.5783 time to fit residues: 75.3499 Evaluate side-chains 121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.0010 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.0170 chunk 32 optimal weight: 0.2980 overall best weight: 0.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112450 restraints weight = 11754.148| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.20 r_work: 0.3302 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6050 Z= 0.127 Angle : 0.552 9.202 8376 Z= 0.279 Chirality : 0.042 0.411 947 Planarity : 0.004 0.042 940 Dihedral : 13.112 73.743 1238 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.99 % Allowed : 17.72 % Favored : 80.29 % 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: 0.17 (0.34), residues: 639 helix: 1.11 (0.44), residues: 147 sheet: -1.19 (0.49), residues: 95 loop : 0.18 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 404 TYR 0.015 0.001 TYR B 420 PHE 0.032 0.002 PHE B 444 TRP 0.011 0.002 TRP B 385 HIS 0.011 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6029) covalent geometry : angle 0.53370 ( 8359) hydrogen bonds : bond 0.03644 ( 201) hydrogen bonds : angle 3.96296 ( 530) metal coordination : bond 0.00908 ( 20) metal coordination : angle 3.20037 ( 17) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8340 (m) cc_final: 0.7957 (m) REVERT: A 58 THR cc_start: 0.8368 (t) cc_final: 0.8156 (p) REVERT: A 66 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 101 THR cc_start: 0.8458 (t) cc_final: 0.8033 (m) REVERT: A 103 CYS cc_start: 0.8381 (m) cc_final: 0.8127 (m) REVERT: A 122 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8496 (mmm) REVERT: B 48 ASP cc_start: 0.7988 (t0) cc_final: 0.7778 (t0) REVERT: B 49 MET cc_start: 0.7961 (ttp) cc_final: 0.7734 (ttp) REVERT: B 57 MET cc_start: 0.8636 (mmt) cc_final: 0.8415 (mmm) REVERT: B 126 ASP cc_start: 0.7878 (m-30) cc_final: 0.7646 (m-30) REVERT: B 154 TYR cc_start: 0.8175 (m-80) cc_final: 0.7883 (m-80) REVERT: B 169 MET cc_start: 0.8492 (ttp) cc_final: 0.8175 (ptm) REVERT: B 254 GLN cc_start: 0.8234 (tt0) cc_final: 0.8022 (tt0) REVERT: B 324 ASP cc_start: 0.7487 (m-30) cc_final: 0.7065 (m-30) REVERT: B 352 ASP cc_start: 0.6631 (t0) cc_final: 0.5994 (t0) REVERT: B 381 VAL cc_start: 0.6829 (p) cc_final: 0.6584 (p) REVERT: B 400 ARG cc_start: 0.8234 (ttt-90) cc_final: 0.7997 (mtp180) REVERT: B 520 TRP cc_start: 0.8179 (m100) cc_final: 0.7918 (m-90) outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 0.6104 time to fit residues: 83.2270 Evaluate side-chains 121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 58 optimal weight: 0.4980 chunk 47 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.0806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113753 restraints weight = 15087.699| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.56 r_work: 0.3308 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6050 Z= 0.095 Angle : 0.522 7.368 8376 Z= 0.263 Chirality : 0.039 0.206 947 Planarity : 0.004 0.041 940 Dihedral : 13.030 73.804 1238 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.45 % Allowed : 19.71 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.34), residues: 639 helix: 1.30 (0.44), residues: 144 sheet: -1.20 (0.49), residues: 93 loop : 0.27 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 492 TYR 0.020 0.001 TYR B 447 PHE 0.022 0.001 PHE B 444 TRP 0.011 0.001 TRP B 227 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6029) covalent geometry : angle 0.51051 ( 8359) hydrogen bonds : bond 0.03218 ( 201) hydrogen bonds : angle 3.77219 ( 530) metal coordination : bond 0.00713 ( 20) metal coordination : angle 2.48700 ( 17) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8306 (m) cc_final: 0.7936 (m) REVERT: A 66 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 57 MET cc_start: 0.8533 (mmt) cc_final: 0.8285 (mmm) REVERT: B 126 ASP cc_start: 0.7642 (m-30) cc_final: 0.7398 (m-30) REVERT: B 154 TYR cc_start: 0.8010 (m-80) cc_final: 0.7793 (m-80) REVERT: B 169 MET cc_start: 0.8347 (ttp) cc_final: 0.8041 (ptm) REVERT: B 231 ILE cc_start: 0.8424 (mm) cc_final: 0.8153 (tp) REVERT: B 324 ASP cc_start: 0.7346 (m-30) cc_final: 0.6941 (m-30) REVERT: B 339 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7413 (ttpt) REVERT: B 381 VAL cc_start: 0.6654 (p) cc_final: 0.6279 (p) REVERT: B 400 ARG cc_start: 0.8097 (ttt-90) cc_final: 0.7876 (mtp180) REVERT: B 492 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7138 (mtm110) REVERT: B 520 TRP cc_start: 0.8080 (m100) cc_final: 0.7823 (m-90) outliers start: 8 outliers final: 2 residues processed: 131 average time/residue: 0.5441 time to fit residues: 74.4671 Evaluate side-chains 119 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 20 optimal weight: 0.2980 chunk 27 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 53 optimal weight: 0.0060 chunk 58 optimal weight: 0.8980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 22 GLN B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111962 restraints weight = 14542.024| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.50 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6050 Z= 0.134 Angle : 0.542 7.744 8376 Z= 0.274 Chirality : 0.040 0.138 947 Planarity : 0.004 0.042 940 Dihedral : 13.052 73.730 1238 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.63 % Allowed : 20.43 % Favored : 77.94 % 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: 0.28 (0.34), residues: 639 helix: 1.26 (0.44), residues: 147 sheet: -1.11 (0.49), residues: 92 loop : 0.21 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 400 TYR 0.015 0.001 TYR B 420 PHE 0.019 0.002 PHE B 133 TRP 0.011 0.001 TRP B 520 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6029) covalent geometry : angle 0.52663 ( 8359) hydrogen bonds : bond 0.03653 ( 201) hydrogen bonds : angle 3.88650 ( 530) metal coordination : bond 0.00779 ( 20) metal coordination : angle 2.91948 ( 17) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8319 (m) cc_final: 0.7960 (m) REVERT: A 66 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 126 ASP cc_start: 0.7566 (m-30) cc_final: 0.7319 (m-30) REVERT: B 154 TYR cc_start: 0.8008 (m-80) cc_final: 0.7744 (m-80) REVERT: B 169 MET cc_start: 0.8356 (ttp) cc_final: 0.8126 (ptm) REVERT: B 324 ASP cc_start: 0.7271 (m-30) cc_final: 0.6868 (m-30) REVERT: B 381 VAL cc_start: 0.6700 (p) cc_final: 0.6265 (p) REVERT: B 400 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7895 (mtp180) REVERT: B 492 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7165 (mtm110) REVERT: B 520 TRP cc_start: 0.8104 (m100) cc_final: 0.7862 (m-90) outliers start: 9 outliers final: 1 residues processed: 127 average time/residue: 0.5778 time to fit residues: 76.6537 Evaluate side-chains 120 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.0870 overall best weight: 0.0686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114499 restraints weight = 16633.658| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.68 r_work: 0.3316 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6050 Z= 0.090 Angle : 0.508 7.293 8376 Z= 0.257 Chirality : 0.038 0.136 947 Planarity : 0.004 0.042 940 Dihedral : 12.991 73.741 1238 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.72 % Allowed : 20.80 % Favored : 78.48 % 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: 0.38 (0.34), residues: 639 helix: 1.35 (0.44), residues: 146 sheet: -1.19 (0.47), residues: 92 loop : 0.32 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 400 TYR 0.022 0.001 TYR B 447 PHE 0.019 0.001 PHE B 444 TRP 0.013 0.001 TRP B 227 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6029) covalent geometry : angle 0.49805 ( 8359) hydrogen bonds : bond 0.03070 ( 201) hydrogen bonds : angle 3.70345 ( 530) metal coordination : bond 0.00704 ( 20) metal coordination : angle 2.23234 ( 17) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8324 (m) cc_final: 0.7970 (m) REVERT: A 66 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 122 MET cc_start: 0.8623 (mmm) cc_final: 0.8408 (mpp) REVERT: B 126 ASP cc_start: 0.7607 (m-30) cc_final: 0.7362 (m-30) REVERT: B 153 MET cc_start: 0.8504 (mmp) cc_final: 0.8239 (mmm) REVERT: B 169 MET cc_start: 0.8367 (ttp) cc_final: 0.8156 (ptm) REVERT: B 231 ILE cc_start: 0.8415 (mm) cc_final: 0.8125 (tp) REVERT: B 324 ASP cc_start: 0.7194 (m-30) cc_final: 0.6823 (m-30) REVERT: B 381 VAL cc_start: 0.6473 (p) cc_final: 0.5983 (p) REVERT: B 400 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7836 (mtp180) REVERT: B 492 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7144 (mtm110) REVERT: B 520 TRP cc_start: 0.8023 (m100) cc_final: 0.7781 (m-90) outliers start: 4 outliers final: 2 residues processed: 127 average time/residue: 0.5534 time to fit residues: 73.4440 Evaluate side-chains 126 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111351 restraints weight = 15974.384| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.62 r_work: 0.3276 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6050 Z= 0.170 Angle : 0.563 7.546 8376 Z= 0.284 Chirality : 0.041 0.178 947 Planarity : 0.004 0.042 940 Dihedral : 13.059 73.844 1238 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.90 % Allowed : 21.34 % Favored : 77.76 % 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: 0.30 (0.34), residues: 639 helix: 1.32 (0.45), residues: 141 sheet: -1.15 (0.49), residues: 92 loop : 0.23 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 400 TYR 0.018 0.001 TYR B 420 PHE 0.020 0.002 PHE B 133 TRP 0.015 0.002 TRP B 520 HIS 0.007 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6029) covalent geometry : angle 0.54499 ( 8359) hydrogen bonds : bond 0.03967 ( 201) hydrogen bonds : angle 3.93915 ( 530) metal coordination : bond 0.00906 ( 20) metal coordination : angle 3.14784 ( 17) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8322 (m) cc_final: 0.7965 (m) REVERT: A 66 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 122 MET cc_start: 0.8640 (mmm) cc_final: 0.8405 (mpp) REVERT: B 47 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (ptpp) REVERT: B 126 ASP cc_start: 0.7615 (m-30) cc_final: 0.7356 (m-30) REVERT: B 324 ASP cc_start: 0.7173 (m-30) cc_final: 0.6785 (m-30) REVERT: B 381 VAL cc_start: 0.6667 (p) cc_final: 0.6297 (p) REVERT: B 492 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7174 (mtm110) REVERT: B 501 MET cc_start: 0.7574 (ttp) cc_final: 0.7289 (ttm) REVERT: B 520 TRP cc_start: 0.8160 (m100) cc_final: 0.7918 (m-90) outliers start: 5 outliers final: 4 residues processed: 131 average time/residue: 0.5536 time to fit residues: 75.8974 Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 432 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 51 optimal weight: 0.0050 chunk 31 optimal weight: 0.2980 chunk 63 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 overall best weight: 0.0132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112650 restraints weight = 21060.171| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.08 r_work: 0.3274 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6050 Z= 0.094 Angle : 0.521 6.631 8376 Z= 0.265 Chirality : 0.038 0.137 947 Planarity : 0.004 0.048 940 Dihedral : 13.030 73.753 1238 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.90 % Allowed : 21.70 % Favored : 77.40 % 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: 0.44 (0.34), residues: 639 helix: 1.52 (0.45), residues: 139 sheet: -1.15 (0.48), residues: 92 loop : 0.32 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.020 0.001 TYR B 447 PHE 0.018 0.001 PHE B 444 TRP 0.013 0.001 TRP B 348 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 6029) covalent geometry : angle 0.50978 ( 8359) hydrogen bonds : bond 0.03318 ( 201) hydrogen bonds : angle 3.76787 ( 530) metal coordination : bond 0.00732 ( 20) metal coordination : angle 2.42162 ( 17) Misc. bond : bond 0.00057 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8308 (m) cc_final: 0.7927 (m) REVERT: A 66 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 122 MET cc_start: 0.8619 (mmm) cc_final: 0.8385 (mpp) REVERT: B 126 ASP cc_start: 0.7647 (m-30) cc_final: 0.7395 (m-30) REVERT: B 153 MET cc_start: 0.8599 (mmp) cc_final: 0.8277 (mmm) REVERT: B 169 MET cc_start: 0.8364 (ttp) cc_final: 0.8081 (ptm) REVERT: B 324 ASP cc_start: 0.7242 (m-30) cc_final: 0.6850 (m-30) REVERT: B 381 VAL cc_start: 0.6675 (p) cc_final: 0.6291 (p) REVERT: B 400 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7909 (mtp180) REVERT: B 520 TRP cc_start: 0.8086 (m100) cc_final: 0.7811 (m-90) outliers start: 5 outliers final: 3 residues processed: 132 average time/residue: 0.5696 time to fit residues: 78.5689 Evaluate side-chains 131 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114499 restraints weight = 9671.187| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.95 r_work: 0.3343 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6050 Z= 0.132 Angle : 0.537 6.822 8376 Z= 0.272 Chirality : 0.039 0.138 947 Planarity : 0.004 0.042 940 Dihedral : 13.024 73.792 1238 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 21.34 % Favored : 77.76 % 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: 0.31 (0.34), residues: 639 helix: 1.41 (0.45), residues: 142 sheet: -1.13 (0.48), residues: 92 loop : 0.20 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.014 0.001 TYR B 420 PHE 0.018 0.001 PHE B 133 TRP 0.011 0.002 TRP B 385 HIS 0.007 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6029) covalent geometry : angle 0.52235 ( 8359) hydrogen bonds : bond 0.03636 ( 201) hydrogen bonds : angle 3.84527 ( 530) metal coordination : bond 0.00786 ( 20) metal coordination : angle 2.77424 ( 17) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.35 seconds wall clock time: 48 minutes 42.02 seconds (2922.02 seconds total)