Starting phenix.real_space_refine on Fri Feb 14 05:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.map" model { file = "/net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psn_13615/02_2025/7psn_13615.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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 10 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6088 2.51 5 N 1604 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B Time building chain proxies: 9.15, per 1000 atoms: 0.97 Number of scatterers: 9464 At special positions: 0 Unit cell: (83.628, 75.348, 141.588, 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) S 34 16.00 P 10 15.00 Mg 2 11.99 O 1726 8.00 N 1604 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 68.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.747A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 233 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 367 removed outlier: 3.583A pdb=" N LEU A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.697A pdb=" N PHE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.593A pdb=" N ILE A 636 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.748A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 233 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 313 through 367 removed outlier: 3.584A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 396 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.696A pdb=" N PHE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.594A pdb=" N ILE B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 676 Processing sheet with id=AA1, first strand: chain 'A' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 457 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU A 439 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 459 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N THR A 437 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 441 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER A 490 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.528A pdb=" N MET A 594 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 629 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 596 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 641 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 642 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 653 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 644 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE B 457 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 439 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 459 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 437 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 441 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 490 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.529A pdb=" N MET B 594 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 629 " --> pdb=" O MET B 594 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 596 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 641 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 642 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 653 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 644 " --> pdb=" O ARG B 651 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1878 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: 3.00 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.43: 2478 1.43 - 1.56: 5568 1.56 - 1.68: 14 1.68 - 1.80: 68 Bond restraints: 9636 Sorted by residual: bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.626 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.625 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C6 ANP A 701 " pdb=" N6 ANP A 701 " ideal model delta sigma weight residual 1.340 1.471 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 12846 2.77 - 5.54: 126 5.54 - 8.30: 28 8.30 - 11.07: 12 11.07 - 13.84: 8 Bond angle restraints: 13020 Sorted by residual: angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.54 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.59 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O3 LOP A 704 " pdb=" P1 LOP A 704 " pdb=" O4 LOP A 704 " ideal model delta sigma weight residual 120.67 109.29 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O3 LOP B 704 " pdb=" P1 LOP B 704 " pdb=" O4 LOP B 704 " ideal model delta sigma weight residual 120.67 109.32 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" O5' ANP A 701 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 5505 25.69 - 51.38: 293 51.38 - 77.07: 44 77.07 - 102.76: 8 102.76 - 128.44: 2 Dihedral angle restraints: 5852 sinusoidal: 2468 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.33 128.44 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.31 128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O2' ANP B 701 " pdb=" C2' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O3' ANP B 701 " ideal model delta sinusoidal sigma weight residual 47.90 -36.39 84.29 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 408 0.072 - 0.108: 114 0.108 - 0.144: 14 0.144 - 0.180: 6 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ANP A 701 " pdb=" C1' ANP A 701 " pdb=" C3' ANP A 701 " pdb=" O2' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ANP B 701 " pdb=" C1' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O2' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C4 LOP A 704 " pdb=" C3 LOP A 704 " pdb=" C5 LOP A 704 " pdb=" O5 LOP A 704 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1493 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP B 703 " 0.204 2.00e-02 2.50e+03 2.05e-01 4.21e+02 pdb=" C14 LOP B 703 " -0.200 2.00e-02 2.50e+03 pdb=" C15 LOP B 703 " -0.210 2.00e-02 2.50e+03 pdb=" C16 LOP B 703 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 703 " -0.204 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C14 LOP A 703 " 0.200 2.00e-02 2.50e+03 pdb=" C15 LOP A 703 " 0.210 2.00e-02 2.50e+03 pdb=" C16 LOP A 703 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 387 " -0.005 2.00e-02 2.50e+03 8.91e-03 7.93e-01 pdb=" C VAL A 387 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 387 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.005 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 70 2.52 - 3.11: 7626 3.11 - 3.71: 14350 3.71 - 4.30: 20897 4.30 - 4.90: 35778 Nonbonded interactions: 78721 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN A 517 " pdb="MG MG A 702 " model vdw 1.923 2.170 nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.963 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.963 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.047 2.170 ... (remaining 78716 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.009 0.224 9636 Z= 0.565 Angle : 0.823 13.840 13020 Z= 0.365 Chirality : 0.042 0.180 1496 Planarity : 0.008 0.205 1620 Dihedral : 15.989 128.445 3668 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.21), residues: 1166 helix: -1.13 (0.16), residues: 772 sheet: -3.80 (0.43), residues: 52 loop : -3.49 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 631 PHE 0.009 0.001 PHE A 179 TYR 0.011 0.002 TYR B 161 ARG 0.002 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.021 Fit side-chains REVERT: A 426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.3500 time to fit residues: 176.5151 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 304 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118304 restraints weight = 10368.782| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.12 r_work: 0.3325 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9636 Z= 0.190 Angle : 0.547 7.487 13020 Z= 0.278 Chirality : 0.041 0.148 1496 Planarity : 0.003 0.028 1620 Dihedral : 11.709 124.533 1470 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.60 % Allowed : 10.88 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1166 helix: 0.68 (0.18), residues: 780 sheet: -2.66 (0.50), residues: 62 loop : -2.64 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 197 PHE 0.012 0.001 PHE A 391 TYR 0.013 0.001 TYR B 161 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 1.029 Fit side-chains REVERT: A 426 LEU cc_start: 0.8321 (mm) cc_final: 0.8088 (mp) REVERT: A 572 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8200 (mmm) REVERT: A 652 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 572 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: B 652 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8369 (mt-10) outliers start: 6 outliers final: 0 residues processed: 116 average time/residue: 1.2837 time to fit residues: 160.8108 Evaluate side-chains 99 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 572 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 618 ASN B 304 ASN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111627 restraints weight = 10655.955| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.17 r_work: 0.3273 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9636 Z= 0.235 Angle : 0.548 7.350 13020 Z= 0.278 Chirality : 0.042 0.154 1496 Planarity : 0.003 0.032 1620 Dihedral : 10.086 113.711 1470 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.10 % Allowed : 13.67 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1166 helix: 1.12 (0.18), residues: 782 sheet: -2.29 (0.55), residues: 62 loop : -2.04 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 671 HIS 0.003 0.001 HIS A 197 PHE 0.014 0.001 PHE A 179 TYR 0.009 0.001 TYR A 269 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.071 Fit side-chains REVERT: A 572 MET cc_start: 0.8438 (mmm) cc_final: 0.8236 (mmm) REVERT: A 652 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 666 LEU cc_start: 0.6956 (tm) cc_final: 0.6739 (tm) REVERT: B 326 MET cc_start: 0.7399 (mmm) cc_final: 0.7182 (mmm) REVERT: B 652 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8189 (mt-10) outliers start: 11 outliers final: 2 residues processed: 129 average time/residue: 1.0538 time to fit residues: 147.7231 Evaluate side-chains 105 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114596 restraints weight = 10692.903| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.10 r_work: 0.3285 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9636 Z= 0.159 Angle : 0.493 6.771 13020 Z= 0.252 Chirality : 0.040 0.147 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.569 109.780 1470 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.10 % Allowed : 14.17 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1166 helix: 1.55 (0.18), residues: 784 sheet: -2.07 (0.57), residues: 62 loop : -1.73 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS A 197 PHE 0.024 0.001 PHE B 350 TYR 0.017 0.001 TYR B 161 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.886 Fit side-chains REVERT: A 556 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7447 (mptt) REVERT: A 581 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 666 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6775 (tm) REVERT: B 326 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7364 (mmm) REVERT: B 556 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7462 (mptt) REVERT: B 572 MET cc_start: 0.8523 (mmm) cc_final: 0.8167 (tpt) REVERT: B 581 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7232 (mp) outliers start: 21 outliers final: 4 residues processed: 130 average time/residue: 1.0834 time to fit residues: 152.8705 Evaluate side-chains 116 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS A 304 ASN B 235 HIS B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113727 restraints weight = 10750.841| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.11 r_work: 0.3252 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9636 Z= 0.169 Angle : 0.492 6.573 13020 Z= 0.250 Chirality : 0.040 0.152 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.260 107.064 1470 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.50 % Allowed : 14.67 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1166 helix: 1.79 (0.18), residues: 786 sheet: -2.34 (0.57), residues: 52 loop : -1.49 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.009 0.001 HIS A 235 PHE 0.017 0.001 PHE B 350 TYR 0.013 0.001 TYR B 667 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.087 Fit side-chains REVERT: A 134 GLN cc_start: 0.6896 (mt0) cc_final: 0.6679 (mt0) REVERT: A 350 PHE cc_start: 0.7347 (t80) cc_final: 0.6714 (t80) REVERT: A 556 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7502 (mptt) REVERT: A 581 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 666 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6757 (tm) REVERT: B 326 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7509 (mmm) REVERT: B 350 PHE cc_start: 0.7371 (t80) cc_final: 0.6745 (t80) REVERT: B 556 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7520 (mptt) REVERT: B 572 MET cc_start: 0.8518 (mmm) cc_final: 0.8160 (tpt) REVERT: B 581 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7265 (mp) outliers start: 25 outliers final: 7 residues processed: 123 average time/residue: 1.0449 time to fit residues: 140.0568 Evaluate side-chains 113 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109364 restraints weight = 10945.765| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.14 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9636 Z= 0.277 Angle : 0.544 6.706 13020 Z= 0.275 Chirality : 0.042 0.162 1496 Planarity : 0.003 0.024 1620 Dihedral : 9.434 108.000 1470 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 15.87 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1166 helix: 1.63 (0.18), residues: 784 sheet: -1.80 (0.59), residues: 62 loop : -1.50 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 463 HIS 0.004 0.001 HIS B 197 PHE 0.016 0.001 PHE B 350 TYR 0.022 0.002 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.082 Fit side-chains REVERT: A 556 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7473 (mptt) REVERT: A 581 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 662 MET cc_start: 0.6747 (tmm) cc_final: 0.6525 (ttt) REVERT: B 134 GLN cc_start: 0.6929 (mt0) cc_final: 0.6699 (mt0) REVERT: B 556 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7486 (mptt) REVERT: B 581 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7310 (mp) REVERT: B 662 MET cc_start: 0.6797 (tmm) cc_final: 0.6576 (ttt) outliers start: 26 outliers final: 8 residues processed: 130 average time/residue: 1.1096 time to fit residues: 155.8989 Evaluate side-chains 117 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111917 restraints weight = 10889.572| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.14 r_work: 0.3254 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9636 Z= 0.184 Angle : 0.500 7.836 13020 Z= 0.255 Chirality : 0.040 0.166 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.223 105.699 1470 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.20 % Allowed : 16.27 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1166 helix: 1.80 (0.18), residues: 786 sheet: -2.17 (0.58), residues: 52 loop : -1.29 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE B 254 TYR 0.030 0.001 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.031 Fit side-chains REVERT: A 350 PHE cc_start: 0.7112 (t80) cc_final: 0.6511 (t80) REVERT: A 556 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7377 (mptt) REVERT: A 662 MET cc_start: 0.6614 (tmm) cc_final: 0.6368 (ttt) REVERT: B 134 GLN cc_start: 0.6724 (mt0) cc_final: 0.6481 (mt0) REVERT: B 350 PHE cc_start: 0.7156 (t80) cc_final: 0.6554 (t80) REVERT: B 556 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7400 (mptt) REVERT: B 572 MET cc_start: 0.8398 (mmm) cc_final: 0.8105 (tpt) REVERT: B 662 MET cc_start: 0.6656 (tmm) cc_final: 0.6411 (ttt) outliers start: 22 outliers final: 8 residues processed: 133 average time/residue: 1.0491 time to fit residues: 151.8094 Evaluate side-chains 119 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111141 restraints weight = 11041.425| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.15 r_work: 0.3229 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9636 Z= 0.192 Angle : 0.507 7.270 13020 Z= 0.258 Chirality : 0.040 0.165 1496 Planarity : 0.003 0.026 1620 Dihedral : 9.190 105.377 1470 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.90 % Allowed : 17.27 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1166 helix: 1.91 (0.18), residues: 782 sheet: -2.18 (0.57), residues: 52 loop : -1.22 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 463 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE B 254 TYR 0.030 0.001 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.147 Fit side-chains REVERT: A 350 PHE cc_start: 0.7255 (t80) cc_final: 0.6680 (t80) REVERT: A 556 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7478 (mptt) REVERT: B 134 GLN cc_start: 0.6859 (mt0) cc_final: 0.6620 (mt0) REVERT: B 350 PHE cc_start: 0.7271 (t80) cc_final: 0.6706 (t80) REVERT: B 556 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7505 (mptt) outliers start: 19 outliers final: 9 residues processed: 125 average time/residue: 1.0435 time to fit residues: 141.8820 Evaluate side-chains 121 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111345 restraints weight = 10916.865| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.15 r_work: 0.3239 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9636 Z= 0.188 Angle : 0.507 8.054 13020 Z= 0.257 Chirality : 0.040 0.162 1496 Planarity : 0.003 0.028 1620 Dihedral : 9.159 104.723 1470 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 17.27 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1166 helix: 1.96 (0.18), residues: 782 sheet: -2.15 (0.58), residues: 52 loop : -1.16 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 463 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE A 179 TYR 0.030 0.001 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.043 Fit side-chains REVERT: A 350 PHE cc_start: 0.7092 (t80) cc_final: 0.6516 (t80) REVERT: A 556 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7391 (mptt) REVERT: B 134 GLN cc_start: 0.6752 (mt0) cc_final: 0.6525 (mt0) REVERT: B 350 PHE cc_start: 0.7108 (t80) cc_final: 0.6558 (t80) REVERT: B 556 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7422 (mptt) REVERT: B 623 SER cc_start: 0.8825 (m) cc_final: 0.8623 (m) outliers start: 21 outliers final: 9 residues processed: 127 average time/residue: 1.1095 time to fit residues: 152.6239 Evaluate side-chains 120 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.0170 chunk 112 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113295 restraints weight = 10888.826| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.15 r_work: 0.3257 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9636 Z= 0.162 Angle : 0.502 8.088 13020 Z= 0.254 Chirality : 0.040 0.176 1496 Planarity : 0.003 0.028 1620 Dihedral : 9.022 103.249 1470 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.30 % Allowed : 18.56 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1166 helix: 2.07 (0.18), residues: 782 sheet: -2.03 (0.58), residues: 52 loop : -1.10 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE A 179 TYR 0.024 0.001 TYR B 161 ARG 0.004 0.000 ARG A 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.908 Fit side-chains REVERT: A 350 PHE cc_start: 0.7167 (t80) cc_final: 0.6657 (t80) REVERT: A 556 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7482 (mptt) REVERT: A 572 MET cc_start: 0.8538 (mmm) cc_final: 0.8289 (tpt) REVERT: B 350 PHE cc_start: 0.7172 (t80) cc_final: 0.6701 (t80) REVERT: B 556 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7498 (mptt) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 1.0792 time to fit residues: 142.9791 Evaluate side-chains 116 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114355 restraints weight = 10856.907| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.12 r_work: 0.3273 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9636 Z= 0.153 Angle : 0.500 8.147 13020 Z= 0.253 Chirality : 0.039 0.172 1496 Planarity : 0.003 0.032 1620 Dihedral : 8.909 101.788 1470 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.60 % Allowed : 18.86 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1166 helix: 2.18 (0.18), residues: 782 sheet: -1.94 (0.59), residues: 52 loop : -1.01 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.005 0.001 HIS A 197 PHE 0.014 0.001 PHE B 179 TYR 0.026 0.001 TYR B 161 ARG 0.007 0.000 ARG B 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5817.28 seconds wall clock time: 103 minutes 39.98 seconds (6219.98 seconds total)