Starting phenix.real_space_refine on Sun May 3 05:23:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1s_38000/05_2026/8x1s_38000.map" } resolution = 2.37 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= 0.002 sd= 0.133 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 P 2 5.49 5 S 42 5.16 5 Cl 4 4.86 5 C 7233 2.51 5 N 1790 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.01s 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: 11015 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5460 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5463 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' CL': 1, 'I2U': 1, 'LPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' CL': 1, 'I2U': 1, 'LPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 3.18, per 1000 atoms: 0.29 Number of scatterers: 11015 At special positions: 0 Unit cell: (88.54, 127.684, 102.52, 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) Cl 4 17.00 S 42 16.00 P 2 15.00 O 1944 8.00 N 1790 7.00 C 7233 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: 1.02 Conformation dependent library (CDL) restraints added in 548.6 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 69.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 99 removed outlier: 5.665A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.713A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.730A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.503A pdb=" N VAL A 201 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.764A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 332 through 366 removed outlier: 5.824A pdb=" N GLY A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.530A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.728A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 483 through 504 removed outlier: 3.697A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 585 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.767A pdb=" N ASN A 638 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.573A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 99 removed outlier: 5.842A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.713A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.915A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 169 through 196 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.588A pdb=" N VAL B 201 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.619A pdb=" N GLN B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 366 removed outlier: 6.018A pdb=" N GLY B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.626A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.697A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 585 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 621 through 625 removed outlier: 4.341A pdb=" N ASP B 624 " --> pdb=" O ASN B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.855A pdb=" N ASN B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.572A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.596A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.876A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.508A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.852A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 588 through 590 703 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1766 1.32 - 1.44: 2911 1.44 - 1.56: 6506 1.56 - 1.69: 5 1.69 - 1.81: 65 Bond restraints: 11253 Sorted by residual: bond pdb=" CD GLN B 672 " pdb=" OE1 GLN B 672 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CD GLN B 672 " pdb=" NE2 GLN B 672 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" C SER B 663 " pdb=" O SER B 663 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.50e+01 bond pdb=" C THR A 517 " pdb=" O THR A 517 " ideal model delta sigma weight residual 1.236 1.202 0.034 9.90e-03 1.02e+04 1.15e+01 bond pdb=" O33 LPE B 802 " pdb=" P LPE B 802 " ideal model delta sigma weight residual 1.673 1.609 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 14841 2.91 - 5.83: 383 5.83 - 8.74: 46 8.74 - 11.65: 12 11.65 - 14.56: 2 Bond angle restraints: 15284 Sorted by residual: angle pdb=" N ILE A 480 " pdb=" CA ILE A 480 " pdb=" C ILE A 480 " ideal model delta sigma weight residual 110.72 118.48 -7.76 1.01e+00 9.80e-01 5.90e+01 angle pdb=" N LYS A 464 " pdb=" CA LYS A 464 " pdb=" C LYS A 464 " ideal model delta sigma weight residual 111.14 119.40 -8.26 1.08e+00 8.57e-01 5.84e+01 angle pdb=" N LEU B 482 " pdb=" CA LEU B 482 " pdb=" C LEU B 482 " ideal model delta sigma weight residual 110.35 100.32 10.03 1.38e+00 5.25e-01 5.29e+01 angle pdb=" N SER B 17 " pdb=" CA SER B 17 " pdb=" C SER B 17 " ideal model delta sigma weight residual 110.52 100.39 10.13 1.48e+00 4.57e-01 4.68e+01 angle pdb=" C VAL B 288 " pdb=" N PRO B 289 " pdb=" CA PRO B 289 " ideal model delta sigma weight residual 119.76 126.75 -6.99 1.03e+00 9.43e-01 4.60e+01 ... (remaining 15279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 6505 29.45 - 58.89: 178 58.89 - 88.34: 17 88.34 - 117.78: 0 117.78 - 147.23: 6 Dihedral angle restraints: 6706 sinusoidal: 2638 harmonic: 4068 Sorted by residual: dihedral pdb=" C THR B 517 " pdb=" N THR B 517 " pdb=" CA THR B 517 " pdb=" CB THR B 517 " ideal model delta harmonic sigma weight residual -122.00 -104.47 -17.53 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" N ARG A 389 " pdb=" C ARG A 389 " pdb=" CA ARG A 389 " pdb=" CB ARG A 389 " ideal model delta harmonic sigma weight residual 122.80 137.06 -14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C ARG A 389 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" CB ARG A 389 " ideal model delta harmonic sigma weight residual -122.60 -136.78 14.18 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1683 0.133 - 0.266: 106 0.266 - 0.399: 19 0.399 - 0.532: 1 0.532 - 0.664: 2 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CA ARG A 389 " pdb=" N ARG A 389 " pdb=" C ARG A 389 " pdb=" CB ARG A 389 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA PHE A 251 " pdb=" N PHE A 251 " pdb=" C PHE A 251 " pdb=" CB PHE A 251 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.68e+00 chirality pdb=" CA THR B 517 " pdb=" N THR B 517 " pdb=" C THR B 517 " pdb=" CB THR B 517 " both_signs ideal model delta sigma weight residual False 2.53 2.97 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1808 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 479 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C THR A 479 " 0.080 2.00e-02 2.50e+03 pdb=" O THR A 479 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE A 480 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 540 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C CYS A 540 " 0.048 2.00e-02 2.50e+03 pdb=" O CYS A 540 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO A 541 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 110 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C PHE A 110 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 110 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 111 " -0.014 2.00e-02 2.50e+03 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2266 2.76 - 3.29: 11007 3.29 - 3.83: 18942 3.83 - 4.36: 24007 4.36 - 4.90: 38433 Nonbonded interactions: 94655 Sorted by model distance: nonbonded pdb=" NE ARG B 569 " pdb=" OD1 ASP B 617 " model vdw 2.224 3.120 nonbonded pdb=" O THR B 335 " pdb=" OG1 THR B 339 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR B 712 " pdb=" OD2 ASP B 715 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 712 " pdb=" OD2 ASP A 715 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.344 3.040 ... (remaining 94650 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' selection = (chain 'B' and (resid 7 through 600 or (resid 601 and (name N or name CA or name \ C or name O or name CB )) or resid 602 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.010 0.100 11253 Z= 0.601 Angle : 1.118 14.565 15284 Z= 0.728 Chirality : 0.076 0.664 1811 Planarity : 0.006 0.047 1896 Dihedral : 14.309 147.230 4078 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.92 % Allowed : 7.83 % Favored : 91.26 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.23 % 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: 0.26 (0.21), residues: 1396 helix: 0.86 (0.16), residues: 894 sheet: 2.59 (0.72), residues: 34 loop : -1.30 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 389 TYR 0.021 0.003 TYR B 9 PHE 0.026 0.002 PHE A 251 TRP 0.012 0.002 TRP A 63 HIS 0.005 0.002 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00986 (11253) covalent geometry : angle 1.11787 (15284) hydrogen bonds : bond 0.16920 ( 703) hydrogen bonds : angle 6.05351 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.403 Fit side-chains REVERT: A 26 LYS cc_start: 0.7606 (tttp) cc_final: 0.7055 (mmmt) REVERT: A 58 PHE cc_start: 0.8160 (t80) cc_final: 0.7897 (t80) REVERT: A 70 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6874 (pmtt) REVERT: A 296 MET cc_start: 0.8403 (mmp) cc_final: 0.8147 (mmm) REVERT: A 312 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7303 (ttm110) REVERT: A 332 ASP cc_start: 0.7603 (m-30) cc_final: 0.7065 (t0) REVERT: A 474 MET cc_start: 0.8440 (mmm) cc_final: 0.7962 (mmm) REVERT: A 609 ASP cc_start: 0.7477 (p0) cc_final: 0.7160 (p0) REVERT: A 629 ILE cc_start: 0.7541 (mt) cc_final: 0.7301 (mt) REVERT: A 643 LYS cc_start: 0.8332 (mttt) cc_final: 0.7995 (mttt) REVERT: A 687 ASP cc_start: 0.7094 (p0) cc_final: 0.6578 (p0) REVERT: A 707 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 26 LYS cc_start: 0.7486 (tttp) cc_final: 0.6913 (mmmt) REVERT: B 58 PHE cc_start: 0.7071 (m-80) cc_final: 0.6710 (t80) REVERT: B 332 ASP cc_start: 0.7336 (m-30) cc_final: 0.7019 (t0) REVERT: B 348 MET cc_start: 0.6834 (mmp) cc_final: 0.6610 (tpp) REVERT: B 405 SER cc_start: 0.7964 (t) cc_final: 0.7694 (m) REVERT: B 621 ASN cc_start: 0.8050 (t0) cc_final: 0.7683 (t0) REVERT: B 687 ASP cc_start: 0.7227 (p0) cc_final: 0.6871 (p0) REVERT: B 688 ASP cc_start: 0.7834 (m-30) cc_final: 0.7514 (m-30) REVERT: B 692 GLU cc_start: 0.6910 (tt0) cc_final: 0.6649 (mt-10) outliers start: 11 outliers final: 4 residues processed: 158 average time/residue: 0.6814 time to fit residues: 115.1377 Evaluate side-chains 112 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain B residue 707 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 8 GLN A 32 HIS A 38 HIS A 48 GLN A 253 GLN A 279 ASN A 311 ASN A 322 ASN A 326 GLN A 495 GLN A 584 GLN A 611 ASN A 714 HIS B 8 GLN B 38 HIS B 48 GLN B 279 ASN B 311 ASN B 322 ASN B 326 GLN B 495 GLN B 513 ASN B 584 GLN B 714 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094765 restraints weight = 10595.416| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.76 r_work: 0.2920 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11253 Z= 0.139 Angle : 0.560 9.423 15284 Z= 0.292 Chirality : 0.042 0.171 1811 Planarity : 0.005 0.052 1896 Dihedral : 10.512 129.750 1564 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 9.99 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.23), residues: 1396 helix: 1.67 (0.17), residues: 896 sheet: 2.92 (0.79), residues: 34 loop : -0.54 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.022 0.002 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.016 0.002 TRP B 72 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00298 (11253) covalent geometry : angle 0.56000 (15284) hydrogen bonds : bond 0.05003 ( 703) hydrogen bonds : angle 4.65026 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.423 Fit side-chains REVERT: A 26 LYS cc_start: 0.7902 (tttp) cc_final: 0.7266 (mmmt) REVERT: A 56 SER cc_start: 0.8051 (t) cc_final: 0.7771 (p) REVERT: A 70 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7129 (pmmt) REVERT: A 332 ASP cc_start: 0.7526 (m-30) cc_final: 0.6848 (t0) REVERT: A 342 ASP cc_start: 0.8301 (m-30) cc_final: 0.8055 (m-30) REVERT: A 495 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: A 618 GLN cc_start: 0.8151 (mm110) cc_final: 0.7731 (mm-40) REVERT: A 630 ASP cc_start: 0.7923 (t70) cc_final: 0.7552 (t0) REVERT: A 643 LYS cc_start: 0.8674 (mttt) cc_final: 0.8423 (mttt) REVERT: A 692 GLU cc_start: 0.7614 (tt0) cc_final: 0.6874 (tm-30) REVERT: B 22 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 26 LYS cc_start: 0.7923 (tttp) cc_final: 0.7278 (mmmt) REVERT: B 56 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7750 (p) REVERT: B 58 PHE cc_start: 0.7472 (m-80) cc_final: 0.7131 (t80) REVERT: B 277 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5692 (mm-30) REVERT: B 312 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7614 (ttm-80) REVERT: B 322 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7226 (m110) REVERT: B 332 ASP cc_start: 0.7539 (m-30) cc_final: 0.6902 (t0) REVERT: B 348 MET cc_start: 0.8014 (mmp) cc_final: 0.7778 (tpp) REVERT: B 495 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8740 (tt0) REVERT: B 621 ASN cc_start: 0.8314 (t0) cc_final: 0.7947 (t0) REVERT: B 692 GLU cc_start: 0.7619 (tt0) cc_final: 0.7252 (tp30) outliers start: 19 outliers final: 6 residues processed: 132 average time/residue: 0.6549 time to fit residues: 92.8512 Evaluate side-chains 114 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 411 GLN A 495 GLN B 322 ASN B 495 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.091191 restraints weight = 10625.722| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.77 r_work: 0.2864 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11253 Z= 0.190 Angle : 0.596 10.439 15284 Z= 0.310 Chirality : 0.044 0.165 1811 Planarity : 0.005 0.053 1896 Dihedral : 10.586 135.510 1557 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 10.49 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.47 (0.23), residues: 1396 helix: 1.62 (0.17), residues: 898 sheet: 2.87 (0.80), residues: 34 loop : -0.40 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.026 0.002 TYR B 9 PHE 0.016 0.002 PHE B 130 TRP 0.013 0.002 TRP A 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00451 (11253) covalent geometry : angle 0.59600 (15284) hydrogen bonds : bond 0.05645 ( 703) hydrogen bonds : angle 4.68158 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.418 Fit side-chains REVERT: A 26 LYS cc_start: 0.7878 (tttp) cc_final: 0.7234 (mmmt) REVERT: A 56 SER cc_start: 0.8255 (t) cc_final: 0.7857 (p) REVERT: A 70 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7394 (ptmm) REVERT: A 332 ASP cc_start: 0.7594 (m-30) cc_final: 0.6899 (t0) REVERT: A 495 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8750 (tt0) REVERT: A 528 ASP cc_start: 0.8526 (m-30) cc_final: 0.8255 (m-30) REVERT: A 687 ASP cc_start: 0.7654 (p0) cc_final: 0.7082 (p0) REVERT: A 692 GLU cc_start: 0.7864 (tt0) cc_final: 0.7111 (tm-30) REVERT: B 22 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 26 LYS cc_start: 0.7984 (tttp) cc_final: 0.7295 (mmmt) REVERT: B 58 PHE cc_start: 0.7609 (m-80) cc_final: 0.7232 (t80) REVERT: B 270 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7285 (tp) REVERT: B 312 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7700 (ttm-80) REVERT: B 332 ASP cc_start: 0.7552 (m-30) cc_final: 0.6866 (t0) REVERT: B 495 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: B 528 ASP cc_start: 0.8492 (m-30) cc_final: 0.8104 (m-30) REVERT: B 579 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7617 (mtt180) REVERT: B 621 ASN cc_start: 0.8411 (t0) cc_final: 0.8051 (t0) REVERT: B 640 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7260 (tm-30) REVERT: B 692 GLU cc_start: 0.7760 (tt0) cc_final: 0.7229 (tm-30) outliers start: 17 outliers final: 7 residues processed: 128 average time/residue: 0.6408 time to fit residues: 88.1863 Evaluate side-chains 118 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 579 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 495 GLN B 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095395 restraints weight = 10644.715| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.76 r_work: 0.2928 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11253 Z= 0.115 Angle : 0.508 9.055 15284 Z= 0.264 Chirality : 0.041 0.177 1811 Planarity : 0.004 0.053 1896 Dihedral : 9.753 121.972 1557 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.08 % Allowed : 10.74 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.81 (0.23), residues: 1396 helix: 1.89 (0.17), residues: 898 sheet: 2.97 (0.83), residues: 34 loop : -0.29 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.018 0.001 TYR B 9 PHE 0.014 0.001 PHE B 130 TRP 0.014 0.001 TRP A 63 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00239 (11253) covalent geometry : angle 0.50833 (15284) hydrogen bonds : bond 0.04498 ( 703) hydrogen bonds : angle 4.38623 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.511 Fit side-chains REVERT: A 26 LYS cc_start: 0.7924 (tttp) cc_final: 0.7237 (mmmt) REVERT: A 56 SER cc_start: 0.8127 (t) cc_final: 0.7846 (p) REVERT: A 68 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7775 (mtp180) REVERT: A 70 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7276 (ptmm) REVERT: A 332 ASP cc_start: 0.7457 (m-30) cc_final: 0.6862 (t0) REVERT: A 495 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: A 528 ASP cc_start: 0.8482 (m-30) cc_final: 0.8234 (m-30) REVERT: A 614 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: A 629 ILE cc_start: 0.7875 (mt) cc_final: 0.7504 (mt) REVERT: A 630 ASP cc_start: 0.7902 (t70) cc_final: 0.7595 (t0) REVERT: A 692 GLU cc_start: 0.7829 (tt0) cc_final: 0.7113 (tm-30) REVERT: B 22 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 26 LYS cc_start: 0.8005 (tttp) cc_final: 0.7232 (mmmt) REVERT: B 56 SER cc_start: 0.8067 (t) cc_final: 0.7755 (p) REVERT: B 58 PHE cc_start: 0.7407 (m-80) cc_final: 0.7003 (t80) REVERT: B 312 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7630 (ttm-80) REVERT: B 332 ASP cc_start: 0.7473 (m-30) cc_final: 0.6779 (t0) REVERT: B 495 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8730 (tt0) REVERT: B 528 ASP cc_start: 0.8460 (m-30) cc_final: 0.8196 (m-30) REVERT: B 640 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7351 (tm-30) REVERT: B 692 GLU cc_start: 0.7710 (tt0) cc_final: 0.7172 (tm-30) REVERT: B 698 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7587 (mt-10) outliers start: 13 outliers final: 3 residues processed: 122 average time/residue: 0.6268 time to fit residues: 82.5462 Evaluate side-chains 117 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 705 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 612 GLN B 454 GLN B 495 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089077 restraints weight = 10606.885| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.75 r_work: 0.2831 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 11253 Z= 0.275 Angle : 0.670 11.358 15284 Z= 0.347 Chirality : 0.048 0.186 1811 Planarity : 0.005 0.053 1896 Dihedral : 11.058 142.098 1557 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.42 % Allowed : 10.57 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.29 (0.22), residues: 1396 helix: 1.43 (0.17), residues: 898 sheet: 3.04 (0.83), residues: 34 loop : -0.37 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 312 TYR 0.030 0.003 TYR A 9 PHE 0.018 0.002 PHE B 130 TRP 0.016 0.002 TRP B 63 HIS 0.004 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00672 (11253) covalent geometry : angle 0.67033 (15284) hydrogen bonds : bond 0.06376 ( 703) hydrogen bonds : angle 4.80798 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.456 Fit side-chains REVERT: A 26 LYS cc_start: 0.7963 (tttp) cc_final: 0.7217 (mmmt) REVERT: A 70 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7401 (ptmm) REVERT: A 332 ASP cc_start: 0.7646 (m-30) cc_final: 0.6879 (t0) REVERT: A 495 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8882 (tt0) REVERT: A 687 ASP cc_start: 0.7694 (p0) cc_final: 0.7340 (p0) REVERT: A 692 GLU cc_start: 0.7895 (tt0) cc_final: 0.7214 (tm-30) REVERT: B 22 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 26 LYS cc_start: 0.7997 (tttp) cc_final: 0.7233 (mmmt) REVERT: B 58 PHE cc_start: 0.7629 (m-80) cc_final: 0.7176 (t80) REVERT: B 312 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7692 (ttm-80) REVERT: B 332 ASP cc_start: 0.7584 (m-30) cc_final: 0.6818 (t0) REVERT: B 495 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: B 528 ASP cc_start: 0.8562 (m-30) cc_final: 0.8302 (m-30) REVERT: B 579 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7529 (mtt180) REVERT: B 640 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7317 (tm-30) REVERT: B 687 ASP cc_start: 0.7714 (p0) cc_final: 0.7372 (p0) REVERT: B 692 GLU cc_start: 0.7808 (tt0) cc_final: 0.7307 (tm-30) outliers start: 17 outliers final: 5 residues processed: 114 average time/residue: 0.6962 time to fit residues: 85.0389 Evaluate side-chains 110 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 579 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 119 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 411 GLN B 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.094378 restraints weight = 10607.180| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.77 r_work: 0.2895 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11253 Z= 0.119 Angle : 0.520 9.192 15284 Z= 0.269 Chirality : 0.041 0.197 1811 Planarity : 0.004 0.054 1896 Dihedral : 10.057 128.149 1557 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.75 % Allowed : 11.16 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.76 (0.23), residues: 1396 helix: 1.82 (0.17), residues: 896 sheet: 3.07 (0.85), residues: 34 loop : -0.20 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 312 TYR 0.019 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00253 (11253) covalent geometry : angle 0.52050 (15284) hydrogen bonds : bond 0.04585 ( 703) hydrogen bonds : angle 4.39755 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.411 Fit side-chains REVERT: A 26 LYS cc_start: 0.7962 (tttp) cc_final: 0.7166 (mmmt) REVERT: A 70 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7354 (ptmm) REVERT: A 495 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: A 630 ASP cc_start: 0.7908 (t70) cc_final: 0.7593 (t0) REVERT: A 687 ASP cc_start: 0.7668 (p0) cc_final: 0.7175 (p0) REVERT: A 692 GLU cc_start: 0.7869 (tt0) cc_final: 0.7153 (tm-30) REVERT: B 22 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 26 LYS cc_start: 0.8039 (tttp) cc_final: 0.7262 (mmmt) REVERT: B 58 PHE cc_start: 0.7455 (m-80) cc_final: 0.7000 (t80) REVERT: B 332 ASP cc_start: 0.7503 (m-30) cc_final: 0.6759 (t0) REVERT: B 495 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8717 (tt0) REVERT: B 528 ASP cc_start: 0.8540 (m-30) cc_final: 0.8298 (m-30) REVERT: B 640 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7370 (tm-30) REVERT: B 692 GLU cc_start: 0.7784 (tt0) cc_final: 0.7314 (tm-30) outliers start: 9 outliers final: 2 residues processed: 112 average time/residue: 0.6394 time to fit residues: 77.1159 Evaluate side-chains 110 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.090442 restraints weight = 10505.419| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.76 r_work: 0.2856 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11253 Z= 0.208 Angle : 0.605 10.604 15284 Z= 0.313 Chirality : 0.045 0.203 1811 Planarity : 0.005 0.054 1896 Dihedral : 10.632 136.813 1556 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 11.32 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.57 (0.22), residues: 1396 helix: 1.63 (0.17), residues: 898 sheet: 3.09 (0.84), residues: 34 loop : -0.22 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 312 TYR 0.027 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00498 (11253) covalent geometry : angle 0.60491 (15284) hydrogen bonds : bond 0.05705 ( 703) hydrogen bonds : angle 4.62222 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.346 Fit side-chains REVERT: A 26 LYS cc_start: 0.7974 (tttp) cc_final: 0.7187 (mmmt) REVERT: A 70 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7377 (ptmm) REVERT: A 332 ASP cc_start: 0.7662 (m-30) cc_final: 0.6860 (t0) REVERT: A 495 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8758 (tt0) REVERT: A 528 ASP cc_start: 0.8477 (m-30) cc_final: 0.8273 (m-30) REVERT: A 630 ASP cc_start: 0.7895 (t70) cc_final: 0.7586 (t0) REVERT: A 687 ASP cc_start: 0.7689 (p0) cc_final: 0.7377 (p0) REVERT: A 692 GLU cc_start: 0.7863 (tt0) cc_final: 0.7186 (tm-30) REVERT: B 22 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 26 LYS cc_start: 0.8024 (tttp) cc_final: 0.7224 (mmmt) REVERT: B 332 ASP cc_start: 0.7502 (m-30) cc_final: 0.6726 (t0) REVERT: B 495 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8850 (tt0) REVERT: B 640 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7396 (tm-30) REVERT: B 687 ASP cc_start: 0.7670 (p0) cc_final: 0.7392 (p0) REVERT: B 692 GLU cc_start: 0.7780 (tt0) cc_final: 0.7268 (tm-30) outliers start: 16 outliers final: 4 residues processed: 120 average time/residue: 0.6572 time to fit residues: 84.6933 Evaluate side-chains 111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 136 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090986 restraints weight = 10534.301| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.73 r_work: 0.2843 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11253 Z= 0.196 Angle : 0.610 11.979 15284 Z= 0.313 Chirality : 0.045 0.257 1811 Planarity : 0.005 0.054 1896 Dihedral : 10.601 136.276 1556 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.75 % Allowed : 11.82 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.52 (0.22), residues: 1396 helix: 1.60 (0.17), residues: 896 sheet: 3.02 (0.83), residues: 34 loop : -0.25 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 312 TYR 0.026 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.004 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00467 (11253) covalent geometry : angle 0.61036 (15284) hydrogen bonds : bond 0.05546 ( 703) hydrogen bonds : angle 4.59906 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.466 Fit side-chains REVERT: A 26 LYS cc_start: 0.7983 (tttp) cc_final: 0.7211 (mmmt) REVERT: A 70 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7360 (ptmm) REVERT: A 332 ASP cc_start: 0.7670 (m-30) cc_final: 0.6912 (t0) REVERT: A 495 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8915 (tt0) REVERT: A 630 ASP cc_start: 0.7896 (t70) cc_final: 0.7602 (t0) REVERT: A 687 ASP cc_start: 0.7671 (p0) cc_final: 0.7363 (p0) REVERT: A 692 GLU cc_start: 0.7893 (tt0) cc_final: 0.7253 (tm-30) REVERT: B 22 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 26 LYS cc_start: 0.8013 (tttp) cc_final: 0.7233 (mmmt) REVERT: B 55 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7747 (mm) REVERT: B 58 PHE cc_start: 0.7854 (m-80) cc_final: 0.7219 (t80) REVERT: B 332 ASP cc_start: 0.7564 (m-30) cc_final: 0.6783 (t0) REVERT: B 495 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: B 579 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7514 (mtt180) REVERT: B 640 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7419 (tm-30) REVERT: B 687 ASP cc_start: 0.7694 (p0) cc_final: 0.7419 (p0) REVERT: B 692 GLU cc_start: 0.7814 (tt0) cc_final: 0.7311 (tm-30) outliers start: 9 outliers final: 5 residues processed: 111 average time/residue: 0.6747 time to fit residues: 80.4202 Evaluate side-chains 113 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 579 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093334 restraints weight = 10438.584| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.74 r_work: 0.2899 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11253 Z= 0.133 Angle : 0.544 10.868 15284 Z= 0.279 Chirality : 0.042 0.250 1811 Planarity : 0.004 0.054 1896 Dihedral : 10.021 127.812 1556 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 11.99 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.79 (0.23), residues: 1396 helix: 1.83 (0.17), residues: 896 sheet: 3.04 (0.85), residues: 34 loop : -0.18 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 312 TYR 0.021 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00294 (11253) covalent geometry : angle 0.54444 (15284) hydrogen bonds : bond 0.04802 ( 703) hydrogen bonds : angle 4.41956 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.443 Fit side-chains REVERT: A 26 LYS cc_start: 0.7994 (tttp) cc_final: 0.7198 (mmmt) REVERT: A 70 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7362 (ptmm) REVERT: A 495 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: A 630 ASP cc_start: 0.7891 (t70) cc_final: 0.7588 (t0) REVERT: A 687 ASP cc_start: 0.7683 (p0) cc_final: 0.7435 (p0) REVERT: A 692 GLU cc_start: 0.7880 (tt0) cc_final: 0.7179 (tm-30) REVERT: B 22 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 26 LYS cc_start: 0.8042 (tttp) cc_final: 0.7237 (mmmt) REVERT: B 55 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 58 PHE cc_start: 0.7840 (m-80) cc_final: 0.7227 (t80) REVERT: B 236 SER cc_start: 0.8648 (m) cc_final: 0.8246 (p) REVERT: B 332 ASP cc_start: 0.7509 (m-30) cc_final: 0.6746 (t0) REVERT: B 495 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: B 640 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7399 (tm-30) REVERT: B 687 ASP cc_start: 0.7691 (p0) cc_final: 0.7464 (p0) REVERT: B 692 GLU cc_start: 0.7790 (tt0) cc_final: 0.7320 (tm-30) outliers start: 9 outliers final: 5 residues processed: 114 average time/residue: 0.6488 time to fit residues: 79.6005 Evaluate side-chains 114 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 705 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092934 restraints weight = 10585.183| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.74 r_work: 0.2898 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11253 Z= 0.142 Angle : 0.548 9.648 15284 Z= 0.282 Chirality : 0.042 0.220 1811 Planarity : 0.004 0.053 1896 Dihedral : 9.858 125.175 1556 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 12.16 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.79 (0.23), residues: 1396 helix: 1.84 (0.17), residues: 896 sheet: 3.04 (0.85), residues: 34 loop : -0.17 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 312 TYR 0.022 0.002 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.015 0.001 TRP B 63 HIS 0.005 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00323 (11253) covalent geometry : angle 0.54830 (15284) hydrogen bonds : bond 0.04902 ( 703) hydrogen bonds : angle 4.42102 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.442 Fit side-chains REVERT: A 26 LYS cc_start: 0.7992 (tttp) cc_final: 0.7199 (mmmt) REVERT: A 70 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7388 (ptmm) REVERT: A 495 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: A 630 ASP cc_start: 0.7923 (t70) cc_final: 0.7607 (t0) REVERT: A 687 ASP cc_start: 0.7672 (p0) cc_final: 0.7433 (p0) REVERT: A 692 GLU cc_start: 0.7899 (tt0) cc_final: 0.7191 (tm-30) REVERT: B 22 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7687 (mm-30) REVERT: B 26 LYS cc_start: 0.8046 (tttp) cc_final: 0.7236 (mmmt) REVERT: B 55 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7659 (mm) REVERT: B 58 PHE cc_start: 0.7850 (m-80) cc_final: 0.7206 (t80) REVERT: B 236 SER cc_start: 0.8601 (m) cc_final: 0.8199 (p) REVERT: B 332 ASP cc_start: 0.7500 (m-30) cc_final: 0.6731 (t0) REVERT: B 495 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8730 (tt0) REVERT: B 640 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7387 (tm-30) REVERT: B 687 ASP cc_start: 0.7687 (p0) cc_final: 0.7456 (p0) REVERT: B 692 GLU cc_start: 0.7797 (tt0) cc_final: 0.7328 (tm-30) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.6434 time to fit residues: 77.5373 Evaluate side-chains 115 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 705 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.092261 restraints weight = 10735.138| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.75 r_work: 0.2861 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11253 Z= 0.166 Angle : 0.580 11.949 15284 Z= 0.297 Chirality : 0.043 0.233 1811 Planarity : 0.004 0.053 1896 Dihedral : 10.059 128.922 1556 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.83 % Allowed : 11.99 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.71 (0.22), residues: 1396 helix: 1.75 (0.17), residues: 896 sheet: 3.06 (0.84), residues: 34 loop : -0.18 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 312 TYR 0.024 0.002 TYR A 9 PHE 0.016 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00389 (11253) covalent geometry : angle 0.57988 (15284) hydrogen bonds : bond 0.05191 ( 703) hydrogen bonds : angle 4.49132 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4296.26 seconds wall clock time: 74 minutes 1.48 seconds (4441.48 seconds total)