Starting phenix.real_space_refine on Fri Mar 15 13:07:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8m_15917/03_2024/8b8m_15917.pdb" } resolution = 3.49 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 77 5.16 5 C 7729 2.51 5 N 1895 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5631 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 31, 'TRANS': 650} Chain breaks: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.55, per 1000 atoms: 0.56 Number of scatterers: 11758 At special positions: 0 Unit cell: (75.516, 115.878, 128.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 77 16.00 O 2051 8.00 N 1895 7.00 C 7729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 64.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.588A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.763A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.955A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.625A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 488 removed outlier: 4.230A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.753A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.060A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.622A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.933A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.680A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.278A pdb=" N SER A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.282A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 875 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.554A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.573A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 475 removed outlier: 3.540A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.560A pdb=" N ILE B 523 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.518A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 removed outlier: 4.321A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 4.270A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.965A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.571A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.391A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 875 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA6, first strand: chain 'B' and resid 657 through 658 removed outlier: 7.111A pdb=" N GLN B 657 " --> pdb=" O ARG B 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 719 hydrogen bonds defined for protein. 2109 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: 3.22 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3571 1.34 - 1.46: 3005 1.46 - 1.58: 5381 1.58 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12072 Sorted by residual: bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.71e-01 bond pdb=" CA HIS A 655 " pdb=" C HIS A 655 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 8.45e-01 bond pdb=" CA GLN B 45 " pdb=" CB GLN B 45 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.21e-02 6.83e+03 8.38e-01 bond pdb=" CA ILE A 342 " pdb=" CB ILE A 342 " ideal model delta sigma weight residual 1.545 1.538 0.008 9.10e-03 1.21e+04 6.96e-01 bond pdb=" CA HIS B 655 " pdb=" C HIS B 655 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.44e-01 ... (remaining 12067 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 335 106.34 - 113.25: 6329 113.25 - 120.17: 4468 120.17 - 127.08: 5079 127.08 - 134.00: 143 Bond angle restraints: 16354 Sorted by residual: angle pdb=" N VAL A 578 " pdb=" CA VAL A 578 " pdb=" C VAL A 578 " ideal model delta sigma weight residual 113.71 110.74 2.97 9.50e-01 1.11e+00 9.77e+00 angle pdb=" C PHE B 358 " pdb=" N TRP B 359 " pdb=" CA TRP B 359 " ideal model delta sigma weight residual 122.62 118.03 4.59 1.56e+00 4.11e-01 8.67e+00 angle pdb=" N ILE A 722 " pdb=" CA ILE A 722 " pdb=" C ILE A 722 " ideal model delta sigma weight residual 112.98 109.60 3.38 1.25e+00 6.40e-01 7.30e+00 angle pdb=" C PRO B 541 " pdb=" N ARG B 542 " pdb=" CA ARG B 542 " ideal model delta sigma weight residual 125.02 129.77 -4.75 1.76e+00 3.23e-01 7.28e+00 angle pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta sigma weight residual 120.82 124.68 -3.86 1.50e+00 4.44e-01 6.61e+00 ... (remaining 16349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 6463 14.95 - 29.90: 485 29.90 - 44.85: 123 44.85 - 59.80: 41 59.80 - 74.75: 5 Dihedral angle restraints: 7117 sinusoidal: 2915 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.16 -40.16 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA LYS A 230 " pdb=" C LYS A 230 " pdb=" N PHE A 231 " pdb=" CA PHE A 231 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA B 571 " pdb=" C ALA B 571 " pdb=" N PHE B 572 " pdb=" CA PHE B 572 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1106 0.030 - 0.060: 444 0.060 - 0.090: 169 0.090 - 0.120: 53 0.120 - 0.150: 6 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CA VAL B 128 " pdb=" N VAL B 128 " pdb=" C VAL B 128 " pdb=" CB VAL B 128 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA PHE A 760 " pdb=" N PHE A 760 " pdb=" C PHE A 760 " pdb=" CB PHE A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ARG B 542 " pdb=" N ARG B 542 " pdb=" C ARG B 542 " pdb=" CB ARG B 542 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1775 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 685 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 686 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 685 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 686 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 598 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " 0.023 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 326 2.70 - 3.25: 12411 3.25 - 3.80: 19602 3.80 - 4.35: 24128 4.35 - 4.90: 40146 Nonbonded interactions: 96613 Sorted by model distance: nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.148 2.440 nonbonded pdb=" OG1 THR A 709 " pdb=" OE1 GLN A 710 " model vdw 2.181 2.440 nonbonded pdb=" O ASN B 104 " pdb=" ND1 HIS B 108 " model vdw 2.212 2.520 nonbonded pdb=" O TYR A 291 " pdb=" NH2 ARG A 713 " model vdw 2.218 2.520 nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A1002 " model vdw 2.229 2.510 ... (remaining 96608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 81 or resid 89 through 120 or resid 122 through \ 149 or resid 202 through 220 or resid 233 through 414 or resid 446 through 475 \ or resid 517 through 875 or resid 1001 through 1003)) selection = (chain 'B' and (resid 43 through 587 or resid 591 through 875 or resid 1001 thro \ ugh 1003)) } 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: 0.730 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: 4.290 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 33.090 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.003 0.039 12072 Z= 0.206 Angle : 0.532 7.855 16354 Z= 0.301 Chirality : 0.039 0.150 1778 Planarity : 0.005 0.049 2028 Dihedral : 12.082 74.750 4387 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.46 % Allowed : 6.88 % Favored : 88.66 % 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: 1.08 (0.23), residues: 1385 helix: 1.87 (0.17), residues: 876 sheet: -0.75 (0.65), residues: 64 loop : -1.47 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 PHE 0.012 0.001 PHE B 560 TYR 0.016 0.001 TYR A 528 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 274 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8410 (pm20) cc_final: 0.7907 (tt0) REVERT: A 145 LYS cc_start: 0.7523 (mttt) cc_final: 0.7072 (mmtm) REVERT: A 196 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4107 (m-80) REVERT: A 309 MET cc_start: 0.9249 (mmm) cc_final: 0.8968 (mmm) REVERT: A 311 LEU cc_start: 0.8846 (tp) cc_final: 0.8599 (tt) REVERT: A 351 GLN cc_start: 0.7491 (mt0) cc_final: 0.7087 (mt0) REVERT: A 409 ASP cc_start: 0.6945 (m-30) cc_final: 0.6308 (t70) REVERT: A 504 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7254 (p) REVERT: A 546 ASP cc_start: 0.7657 (m-30) cc_final: 0.7451 (m-30) REVERT: A 553 MET cc_start: 0.7918 (tpp) cc_final: 0.7131 (tpp) REVERT: A 585 VAL cc_start: 0.8823 (t) cc_final: 0.8600 (p) REVERT: A 619 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7396 (t-100) REVERT: A 773 MET cc_start: 0.8373 (mmm) cc_final: 0.6102 (mmm) REVERT: B 204 PHE cc_start: 0.6692 (m-80) cc_final: 0.6304 (m-10) REVERT: B 205 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 355 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7432 (tt) REVERT: B 474 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7178 (mp) REVERT: B 528 TYR cc_start: 0.7881 (m-10) cc_final: 0.7473 (m-80) REVERT: B 559 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8928 (mm-40) REVERT: B 587 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6871 (tp) REVERT: B 645 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5544 (tptt) REVERT: B 714 MET cc_start: 0.7320 (mtm) cc_final: 0.6673 (mtm) REVERT: B 774 ASP cc_start: 0.8265 (p0) cc_final: 0.8025 (p0) REVERT: B 832 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 57 outliers final: 18 residues processed: 321 average time/residue: 0.2356 time to fit residues: 106.7452 Evaluate side-chains 203 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 205 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 544 GLN A 632 ASN A 657 GLN A 730 GLN A 814 ASN B 129 HIS B 308 GLN B 351 GLN B 559 GLN B 710 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12072 Z= 0.198 Angle : 0.582 10.730 16354 Z= 0.303 Chirality : 0.041 0.340 1778 Planarity : 0.005 0.061 2028 Dihedral : 7.113 59.727 1617 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.30 % Allowed : 13.21 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.99 (0.23), residues: 1385 helix: 1.83 (0.17), residues: 876 sheet: -0.93 (0.62), residues: 74 loop : -1.55 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.004 0.001 HIS B 108 PHE 0.020 0.001 PHE B 461 TYR 0.037 0.001 TYR A 305 ARG 0.009 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 187 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8495 (mm-40) REVERT: A 125 PHE cc_start: 0.7432 (m-80) cc_final: 0.7182 (m-80) REVERT: A 140 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5757 (mm-30) REVERT: A 145 LYS cc_start: 0.7460 (mttt) cc_final: 0.7198 (mmtm) REVERT: A 196 TYR cc_start: 0.5109 (OUTLIER) cc_final: 0.4337 (m-80) REVERT: A 234 ASN cc_start: 0.7859 (t0) cc_final: 0.7645 (t0) REVERT: A 309 MET cc_start: 0.9175 (mmm) cc_final: 0.8972 (mmm) REVERT: A 355 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 409 ASP cc_start: 0.6844 (m-30) cc_final: 0.6284 (t70) REVERT: A 546 ASP cc_start: 0.7682 (m-30) cc_final: 0.7450 (m-30) REVERT: A 553 MET cc_start: 0.7869 (tpp) cc_final: 0.7108 (tpp) REVERT: A 585 VAL cc_start: 0.8884 (t) cc_final: 0.8673 (p) REVERT: A 619 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.7434 (t-100) REVERT: A 773 MET cc_start: 0.8441 (mmm) cc_final: 0.6315 (mmm) REVERT: A 810 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7274 (tmm160) REVERT: B 528 TYR cc_start: 0.7826 (m-10) cc_final: 0.7553 (m-80) REVERT: B 559 GLN cc_start: 0.9062 (mm110) cc_final: 0.8861 (mm-40) REVERT: B 587 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6820 (tp) REVERT: B 774 ASP cc_start: 0.8388 (p0) cc_final: 0.8129 (p0) REVERT: B 832 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8738 (mp) outliers start: 55 outliers final: 29 residues processed: 225 average time/residue: 0.2129 time to fit residues: 71.3213 Evaluate side-chains 204 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 275 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 814 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12072 Z= 0.245 Angle : 0.585 9.878 16354 Z= 0.304 Chirality : 0.041 0.333 1778 Planarity : 0.005 0.069 2028 Dihedral : 6.377 59.706 1597 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.30 % Allowed : 14.31 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1385 helix: 1.79 (0.17), residues: 878 sheet: -1.19 (0.58), residues: 84 loop : -1.66 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 PHE 0.024 0.002 PHE A 382 TYR 0.040 0.002 TYR A 305 ARG 0.005 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 177 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7460 (mttt) cc_final: 0.7182 (mmtm) REVERT: A 196 TYR cc_start: 0.5162 (OUTLIER) cc_final: 0.4175 (m-80) REVERT: A 234 ASN cc_start: 0.7930 (t0) cc_final: 0.7724 (t0) REVERT: A 355 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7591 (pp) REVERT: A 409 ASP cc_start: 0.6889 (m-30) cc_final: 0.6321 (t70) REVERT: A 546 ASP cc_start: 0.7650 (m-30) cc_final: 0.7444 (m-30) REVERT: A 553 MET cc_start: 0.7961 (tpp) cc_final: 0.7164 (tpp) REVERT: A 585 VAL cc_start: 0.8906 (t) cc_final: 0.8695 (p) REVERT: A 619 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.7300 (t-100) REVERT: A 730 GLN cc_start: 0.8728 (mt0) cc_final: 0.8357 (mt0) REVERT: A 810 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7142 (tmm160) REVERT: B 528 TYR cc_start: 0.7954 (m-10) cc_final: 0.7620 (m-80) REVERT: B 559 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8853 (mm-40) REVERT: B 587 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6833 (tp) REVERT: B 774 ASP cc_start: 0.8432 (p0) cc_final: 0.8184 (p0) REVERT: B 832 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8724 (mp) outliers start: 55 outliers final: 37 residues processed: 215 average time/residue: 0.2026 time to fit residues: 65.5549 Evaluate side-chains 199 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 832 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN B 351 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12072 Z= 0.189 Angle : 0.561 10.410 16354 Z= 0.288 Chirality : 0.041 0.319 1778 Planarity : 0.005 0.070 2028 Dihedral : 6.299 59.720 1595 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.07 % Allowed : 15.95 % Favored : 79.98 % 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: 0.93 (0.23), residues: 1385 helix: 1.81 (0.17), residues: 879 sheet: -1.11 (0.58), residues: 83 loop : -1.63 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.002 0.001 HIS B 844 PHE 0.024 0.001 PHE B 558 TYR 0.018 0.001 TYR A 305 ARG 0.004 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 171 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7904 (t0) cc_final: 0.7686 (t0) REVERT: A 243 LYS cc_start: 0.8940 (tppt) cc_final: 0.8551 (mmtm) REVERT: A 546 ASP cc_start: 0.7654 (m-30) cc_final: 0.7445 (m-30) REVERT: A 553 MET cc_start: 0.7930 (tpp) cc_final: 0.7159 (tpp) REVERT: A 585 VAL cc_start: 0.8912 (t) cc_final: 0.8707 (p) REVERT: A 619 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.7298 (t-100) REVERT: A 730 GLN cc_start: 0.8708 (mt0) cc_final: 0.8334 (mt0) REVERT: A 810 ARG cc_start: 0.7363 (ttp80) cc_final: 0.7103 (tmm160) REVERT: B 95 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8109 (mmtt) REVERT: B 455 LEU cc_start: 0.7742 (tt) cc_final: 0.7541 (pp) REVERT: B 528 TYR cc_start: 0.7919 (m-10) cc_final: 0.7607 (m-80) REVERT: B 559 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8833 (mm-40) REVERT: B 587 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6853 (tp) REVERT: B 774 ASP cc_start: 0.8427 (p0) cc_final: 0.8162 (p0) REVERT: B 801 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7049 (mm) outliers start: 52 outliers final: 34 residues processed: 207 average time/residue: 0.2064 time to fit residues: 64.4603 Evaluate side-chains 199 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12072 Z= 0.352 Angle : 0.654 12.174 16354 Z= 0.342 Chirality : 0.043 0.332 1778 Planarity : 0.005 0.069 2028 Dihedral : 6.161 59.051 1590 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.00 % Allowed : 16.34 % Favored : 78.66 % 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: 0.61 (0.22), residues: 1385 helix: 1.58 (0.17), residues: 874 sheet: -1.31 (0.56), residues: 83 loop : -1.75 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 389 HIS 0.005 0.001 HIS A 818 PHE 0.025 0.002 PHE B 558 TYR 0.028 0.002 TYR A 305 ARG 0.005 0.001 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 162 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7867 (t0) cc_final: 0.7632 (t0) REVERT: A 242 TYR cc_start: 0.7339 (m-80) cc_final: 0.7090 (m-10) REVERT: A 243 LYS cc_start: 0.9025 (tppt) cc_final: 0.8595 (mmtm) REVERT: A 409 ASP cc_start: 0.7143 (m-30) cc_final: 0.6386 (t0) REVERT: A 546 ASP cc_start: 0.7709 (m-30) cc_final: 0.7500 (m-30) REVERT: A 548 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 553 MET cc_start: 0.8025 (tpp) cc_final: 0.7215 (tpp) REVERT: A 585 VAL cc_start: 0.9006 (t) cc_final: 0.8797 (p) REVERT: A 619 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7317 (t-100) REVERT: A 730 GLN cc_start: 0.8767 (mt0) cc_final: 0.8378 (mt0) REVERT: A 773 MET cc_start: 0.8263 (mmm) cc_final: 0.8046 (tpt) REVERT: A 810 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7159 (tmm160) REVERT: B 242 TYR cc_start: 0.8759 (m-10) cc_final: 0.8145 (m-80) REVERT: B 455 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7492 (pp) REVERT: B 559 GLN cc_start: 0.9271 (mm-40) cc_final: 0.9023 (mm-40) REVERT: B 587 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6885 (tp) REVERT: B 801 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6873 (mm) outliers start: 64 outliers final: 45 residues processed: 211 average time/residue: 0.1903 time to fit residues: 61.7330 Evaluate side-chains 200 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 801 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12072 Z= 0.185 Angle : 0.588 14.406 16354 Z= 0.296 Chirality : 0.040 0.338 1778 Planarity : 0.005 0.073 2028 Dihedral : 6.041 59.524 1590 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.60 % Allowed : 18.06 % Favored : 78.34 % 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: 0.80 (0.23), residues: 1385 helix: 1.73 (0.17), residues: 873 sheet: -1.15 (0.57), residues: 83 loop : -1.69 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.003 0.001 HIS A 143 PHE 0.032 0.002 PHE B 558 TYR 0.043 0.002 TYR B 528 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.5888 (mmtm) cc_final: 0.5125 (mmpt) REVERT: A 234 ASN cc_start: 0.7909 (t0) cc_final: 0.7672 (t0) REVERT: A 242 TYR cc_start: 0.7217 (m-80) cc_final: 0.6980 (m-10) REVERT: A 243 LYS cc_start: 0.8927 (tppt) cc_final: 0.8501 (mmtm) REVERT: A 409 ASP cc_start: 0.7025 (m-30) cc_final: 0.6358 (t0) REVERT: A 534 MET cc_start: 0.8330 (mmp) cc_final: 0.7870 (mpp) REVERT: A 546 ASP cc_start: 0.7700 (m-30) cc_final: 0.7488 (m-30) REVERT: A 553 MET cc_start: 0.7974 (tpp) cc_final: 0.7598 (tpp) REVERT: A 585 VAL cc_start: 0.8994 (t) cc_final: 0.8779 (p) REVERT: A 619 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.7165 (t-100) REVERT: A 730 GLN cc_start: 0.8713 (mt0) cc_final: 0.8346 (mt0) REVERT: B 455 LEU cc_start: 0.7969 (tt) cc_final: 0.7710 (pp) REVERT: B 528 TYR cc_start: 0.7812 (m-80) cc_final: 0.7416 (m-80) REVERT: B 587 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6770 (tp) REVERT: B 773 MET cc_start: 0.7911 (mmm) cc_final: 0.7632 (tpp) outliers start: 46 outliers final: 36 residues processed: 204 average time/residue: 0.1938 time to fit residues: 60.3495 Evaluate side-chains 198 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12072 Z= 0.227 Angle : 0.607 14.107 16354 Z= 0.308 Chirality : 0.041 0.361 1778 Planarity : 0.005 0.067 2028 Dihedral : 6.031 59.609 1590 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.60 % Allowed : 18.76 % Favored : 77.64 % 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: 0.79 (0.23), residues: 1385 helix: 1.74 (0.17), residues: 873 sheet: -1.11 (0.57), residues: 83 loop : -1.74 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 650 HIS 0.002 0.001 HIS A 655 PHE 0.021 0.002 PHE B 558 TYR 0.040 0.002 TYR A 305 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7919 (t0) cc_final: 0.7678 (t0) REVERT: A 242 TYR cc_start: 0.7270 (m-80) cc_final: 0.7036 (m-10) REVERT: A 243 LYS cc_start: 0.8912 (tppt) cc_final: 0.8522 (mmtm) REVERT: A 409 ASP cc_start: 0.7075 (m-30) cc_final: 0.6344 (t0) REVERT: A 546 ASP cc_start: 0.7724 (m-30) cc_final: 0.7501 (m-30) REVERT: A 553 MET cc_start: 0.7986 (tpp) cc_final: 0.7607 (tpp) REVERT: A 585 VAL cc_start: 0.9014 (t) cc_final: 0.8798 (p) REVERT: A 619 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7268 (t-100) REVERT: A 730 GLN cc_start: 0.8752 (mt0) cc_final: 0.8354 (mt0) REVERT: B 374 PHE cc_start: 0.7801 (m-10) cc_final: 0.7319 (m-80) REVERT: B 455 LEU cc_start: 0.7469 (tt) cc_final: 0.7245 (pp) REVERT: B 528 TYR cc_start: 0.7896 (m-80) cc_final: 0.7610 (m-80) REVERT: B 587 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6826 (tp) REVERT: B 773 MET cc_start: 0.7871 (mmm) cc_final: 0.7659 (tpp) outliers start: 46 outliers final: 40 residues processed: 193 average time/residue: 0.1840 time to fit residues: 55.1647 Evaluate side-chains 199 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12072 Z= 0.280 Angle : 0.627 13.400 16354 Z= 0.323 Chirality : 0.042 0.333 1778 Planarity : 0.005 0.069 2028 Dihedral : 6.105 59.455 1590 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.91 % Allowed : 19.08 % Favored : 77.01 % 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: 0.79 (0.22), residues: 1385 helix: 1.66 (0.17), residues: 873 sheet: -0.71 (0.62), residues: 64 loop : -1.62 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 650 HIS 0.004 0.001 HIS B 844 PHE 0.024 0.002 PHE A 382 TYR 0.030 0.002 TYR A 305 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7925 (t0) cc_final: 0.7673 (t0) REVERT: A 242 TYR cc_start: 0.7379 (m-80) cc_final: 0.7133 (m-10) REVERT: A 349 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7849 (m) REVERT: A 409 ASP cc_start: 0.7205 (m-30) cc_final: 0.6398 (t0) REVERT: A 546 ASP cc_start: 0.7729 (m-30) cc_final: 0.7504 (m-30) REVERT: A 553 MET cc_start: 0.7963 (tpp) cc_final: 0.7608 (tpp) REVERT: A 585 VAL cc_start: 0.9021 (t) cc_final: 0.8781 (p) REVERT: A 619 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7261 (t-100) REVERT: A 730 GLN cc_start: 0.8764 (mt0) cc_final: 0.8371 (mt0) REVERT: A 773 MET cc_start: 0.8261 (mmm) cc_final: 0.8024 (tpt) REVERT: B 455 LEU cc_start: 0.7391 (tt) cc_final: 0.7183 (pp) REVERT: B 528 TYR cc_start: 0.7832 (m-80) cc_final: 0.7430 (m-80) REVERT: B 587 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6860 (tp) REVERT: B 714 MET cc_start: 0.6790 (mtp) cc_final: 0.6508 (mtp) outliers start: 50 outliers final: 40 residues processed: 193 average time/residue: 0.1964 time to fit residues: 57.9996 Evaluate side-chains 197 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.0570 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 328 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12072 Z= 0.191 Angle : 0.610 14.296 16354 Z= 0.309 Chirality : 0.041 0.356 1778 Planarity : 0.005 0.063 2028 Dihedral : 5.789 54.341 1586 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.44 % Allowed : 19.70 % Favored : 76.86 % 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: 0.88 (0.23), residues: 1385 helix: 1.76 (0.17), residues: 870 sheet: -0.84 (0.61), residues: 73 loop : -1.59 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 650 HIS 0.003 0.001 HIS A 655 PHE 0.024 0.002 PHE A 382 TYR 0.032 0.002 TYR B 305 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7948 (t0) cc_final: 0.7712 (t0) REVERT: A 242 TYR cc_start: 0.7246 (m-80) cc_final: 0.7009 (m-10) REVERT: A 349 CYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7724 (m) REVERT: A 361 LEU cc_start: 0.8918 (tp) cc_final: 0.8543 (tp) REVERT: A 409 ASP cc_start: 0.7078 (m-30) cc_final: 0.6323 (t0) REVERT: A 534 MET cc_start: 0.8214 (mmp) cc_final: 0.7846 (mpp) REVERT: A 553 MET cc_start: 0.7965 (tpp) cc_final: 0.7592 (tpp) REVERT: A 585 VAL cc_start: 0.8984 (t) cc_final: 0.8757 (p) REVERT: A 619 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.7224 (t-100) REVERT: A 730 GLN cc_start: 0.8706 (mt0) cc_final: 0.8344 (mt0) REVERT: B 455 LEU cc_start: 0.7409 (tt) cc_final: 0.7201 (pp) REVERT: B 528 TYR cc_start: 0.7984 (m-80) cc_final: 0.7650 (m-80) REVERT: B 587 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6931 (tp) REVERT: B 714 MET cc_start: 0.6795 (mtp) cc_final: 0.6369 (mtp) outliers start: 44 outliers final: 38 residues processed: 199 average time/residue: 0.1910 time to fit residues: 58.2459 Evaluate side-chains 205 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.0060 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 12072 Z= 0.181 Angle : 0.609 13.887 16354 Z= 0.307 Chirality : 0.041 0.366 1778 Planarity : 0.004 0.062 2028 Dihedral : 5.735 55.939 1586 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.28 % Allowed : 19.86 % Favored : 76.86 % 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: 0.99 (0.23), residues: 1385 helix: 1.80 (0.17), residues: 870 sheet: -0.36 (0.64), residues: 63 loop : -1.53 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.003 0.001 HIS B 129 PHE 0.028 0.002 PHE A 382 TYR 0.032 0.001 TYR B 528 ARG 0.006 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7855 (t0) cc_final: 0.7590 (t0) REVERT: A 242 TYR cc_start: 0.7219 (m-80) cc_final: 0.7003 (m-10) REVERT: A 349 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (m) REVERT: A 361 LEU cc_start: 0.8875 (tp) cc_final: 0.8454 (tp) REVERT: A 409 ASP cc_start: 0.7032 (m-30) cc_final: 0.6290 (t70) REVERT: A 534 MET cc_start: 0.8241 (mmp) cc_final: 0.7856 (mpp) REVERT: A 553 MET cc_start: 0.7948 (tpp) cc_final: 0.7586 (tpp) REVERT: A 585 VAL cc_start: 0.8976 (t) cc_final: 0.8747 (p) REVERT: A 619 TRP cc_start: 0.7704 (OUTLIER) cc_final: 0.7197 (t-100) REVERT: A 730 GLN cc_start: 0.8671 (mt0) cc_final: 0.8344 (mt0) REVERT: B 455 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7191 (pp) REVERT: B 528 TYR cc_start: 0.8049 (m-80) cc_final: 0.7717 (m-80) REVERT: B 587 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6859 (tp) outliers start: 42 outliers final: 35 residues processed: 197 average time/residue: 0.1974 time to fit residues: 59.3997 Evaluate side-chains 204 residues out of total 1279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 549 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111650 restraints weight = 27173.536| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.27 r_work: 0.3507 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12072 Z= 0.187 Angle : 0.610 13.993 16354 Z= 0.307 Chirality : 0.041 0.352 1778 Planarity : 0.004 0.061 2028 Dihedral : 5.691 57.264 1586 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.44 % Allowed : 19.70 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1385 helix: 1.86 (0.17), residues: 870 sheet: -0.39 (0.63), residues: 64 loop : -1.51 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 650 HIS 0.003 0.001 HIS B 129 PHE 0.039 0.002 PHE A 382 TYR 0.031 0.002 TYR B 528 ARG 0.007 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.22 seconds wall clock time: 44 minutes 46.33 seconds (2686.33 seconds total)