Starting phenix.real_space_refine on Wed Feb 4 13:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qio_53192/02_2026/9qio_53192.map" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 P 9 5.49 5 S 50 5.16 5 C 6623 2.51 5 N 1760 2.21 5 O 1991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10433 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2346 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain: "B" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8020 Classifications: {'peptide': 1012} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 956} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.34, per 1000 atoms: 0.22 Number of scatterers: 10433 At special positions: 0 Unit cell: (84.975, 103.95, 134.475, 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) S 50 16.00 P 9 15.00 O 1991 8.00 N 1760 7.00 C 6623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 498.9 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 49.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 4522 through 4536 removed outlier: 4.527A pdb=" N GLU A4526 " --> pdb=" O LYS A4522 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A4534 " --> pdb=" O ALA A4530 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A4535 " --> pdb=" O VAL A4531 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4566 removed outlier: 3.587A pdb=" N LYS A4564 " --> pdb=" O MET A4560 " (cutoff:3.500A) Processing helix chain 'A' and resid 4571 through 4589 Processing helix chain 'A' and resid 4687 through 4699 Processing helix chain 'A' and resid 4704 through 4708 removed outlier: 3.623A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4738 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4762 Processing helix chain 'A' and resid 4762 through 4781 Processing helix chain 'A' and resid 4785 through 4811 Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.030A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.512A pdb=" N LEU B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 102' Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.729A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 4.047A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 301 through 307 removed outlier: 4.076A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 340 removed outlier: 4.623A pdb=" N LEU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.001A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 443 through 451 removed outlier: 3.546A pdb=" N CYS B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.954A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.944A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.553A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 790 removed outlier: 3.600A pdb=" N GLU B 789 " --> pdb=" O ASN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 834 removed outlier: 3.506A pdb=" N GLU B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.728A pdb=" N LEU B 904 " --> pdb=" O THR B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.682A pdb=" N LEU B1005 " --> pdb=" O HIS B1001 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1013 Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4539 removed outlier: 3.716A pdb=" N CYS A4601 " --> pdb=" O ASP A4538 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A4596 " --> pdb=" O THR A4614 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4544 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.386A pdb=" N VAL B 88 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER B 138 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 90 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 64 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS B 91 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS B 63 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N VAL B 158 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE B 65 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 160 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 67 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 419 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 5.661A pdb=" N ILE B 250 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY B 285 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY B 286 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.268A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 591 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.715A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.489A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.489A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1437 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: 2.17 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3390 1.34 - 1.46: 1788 1.46 - 1.57: 5413 1.57 - 1.69: 11 1.69 - 1.81: 73 Bond restraints: 10675 Sorted by residual: bond pdb=" CG1 ILE B 910 " pdb=" CD1 ILE B 910 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA LYS B 368 " pdb=" CB LYS B 368 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.08e+00 bond pdb=" C ARG A4605 " pdb=" N LEU A4606 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.29e-02 6.01e+03 8.41e-01 bond pdb=" C SER B 874 " pdb=" N ILE B 875 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.42e-02 4.96e+03 8.27e-01 bond pdb=" CA THR A4648 " pdb=" C THR A4648 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.43e-02 4.89e+03 8.15e-01 ... (remaining 10670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 14029 1.44 - 2.89: 386 2.89 - 4.33: 63 4.33 - 5.77: 11 5.77 - 7.22: 2 Bond angle restraints: 14491 Sorted by residual: angle pdb=" N GLY A4650 " pdb=" CA GLY A4650 " pdb=" C GLY A4650 " ideal model delta sigma weight residual 115.30 110.38 4.92 1.39e+00 5.18e-01 1.25e+01 angle pdb=" C GLN A4743 " pdb=" N ILE A4744 " pdb=" CA ILE A4744 " ideal model delta sigma weight residual 122.35 118.29 4.06 1.18e+00 7.18e-01 1.19e+01 angle pdb=" CA GLU A4604 " pdb=" CB GLU A4604 " pdb=" CG GLU A4604 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C GLU A4604 " pdb=" CA GLU A4604 " pdb=" CB GLU A4604 " ideal model delta sigma weight residual 110.37 115.04 -4.67 1.64e+00 3.72e-01 8.12e+00 angle pdb=" N ILE B 191 " pdb=" CA ILE B 191 " pdb=" C ILE B 191 " ideal model delta sigma weight residual 111.91 109.58 2.33 8.90e-01 1.26e+00 6.87e+00 ... (remaining 14486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 5908 16.02 - 32.04: 473 32.04 - 48.06: 89 48.06 - 64.08: 27 64.08 - 80.10: 16 Dihedral angle restraints: 6513 sinusoidal: 2689 harmonic: 3824 Sorted by residual: dihedral pdb=" CA TYR B 710 " pdb=" C TYR B 710 " pdb=" N PHE B 711 " pdb=" CA PHE B 711 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU A4545 " pdb=" C GLU A4545 " pdb=" N ASP A4546 " pdb=" CA ASP A4546 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL B 990 " pdb=" C VAL B 990 " pdb=" N LYS B 991 " pdb=" CA LYS B 991 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1057 0.030 - 0.060: 346 0.060 - 0.090: 134 0.090 - 0.121: 72 0.121 - 0.151: 10 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CB ILE B 946 " pdb=" CA ILE B 946 " pdb=" CG1 ILE B 946 " pdb=" CG2 ILE B 946 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA SER B 388 " pdb=" N SER B 388 " pdb=" C SER B 388 " pdb=" CB SER B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB ILE B 250 " pdb=" CA ILE B 250 " pdb=" CG1 ILE B 250 " pdb=" CG2 ILE B 250 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1616 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 267 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 268 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 546 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 547 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A4656 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A4657 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A4657 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A4657 " 0.025 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5741 3.00 - 3.47: 11679 3.47 - 3.95: 18410 3.95 - 4.42: 21094 4.42 - 4.90: 31928 Nonbonded interactions: 88852 Sorted by model distance: nonbonded pdb=" N MET A4542 " pdb=" OD1 ASP A4602 " model vdw 2.525 3.120 nonbonded pdb=" OE2 GLU B 908 " pdb=" O LYS B 922 " model vdw 2.546 3.040 nonbonded pdb=" O ILE B 471 " pdb=" OE2 GLU B 474 " model vdw 2.571 3.040 nonbonded pdb=" OE1 GLN B 400 " pdb=" OG1 THR B 896 " model vdw 2.598 3.040 nonbonded pdb=" O LEU A4797 " pdb=" OG1 THR A4801 " model vdw 2.601 3.040 ... (remaining 88847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 0.002 0.042 10675 Z= 0.123 Angle : 0.586 7.217 14491 Z= 0.339 Chirality : 0.040 0.151 1619 Planarity : 0.004 0.047 1858 Dihedral : 12.970 80.097 4029 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1301 helix: 1.62 (0.22), residues: 559 sheet: 0.05 (0.39), residues: 176 loop : -0.05 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 809 TYR 0.012 0.001 TYR B1045 PHE 0.016 0.001 PHE B 711 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS A4756 Details of bonding type rmsd covalent geometry : bond 0.00229 (10675) covalent geometry : angle 0.58567 (14491) hydrogen bonds : bond 0.14393 ( 509) hydrogen bonds : angle 6.86079 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7720 (mmp) cc_final: 0.7072 (mmm) REVERT: A 4598 PHE cc_start: 0.9400 (m-80) cc_final: 0.8907 (m-80) REVERT: A 4609 MET cc_start: 0.9761 (tpt) cc_final: 0.9467 (tpp) REVERT: A 4613 ILE cc_start: 0.9635 (mm) cc_final: 0.9031 (tp) REVERT: A 4628 PHE cc_start: 0.9143 (m-80) cc_final: 0.8818 (m-80) REVERT: A 4700 LEU cc_start: 0.9419 (mt) cc_final: 0.9191 (mt) REVERT: B 69 MET cc_start: 0.8728 (mmm) cc_final: 0.8513 (mmm) REVERT: B 271 PHE cc_start: 0.9789 (p90) cc_final: 0.9122 (p90) REVERT: B 476 LEU cc_start: 0.9876 (tp) cc_final: 0.9668 (tp) REVERT: B 909 MET cc_start: 0.9701 (tmm) cc_final: 0.9496 (tmm) REVERT: B 1009 MET cc_start: 0.9009 (mmp) cc_final: 0.8462 (mmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1144 time to fit residues: 9.9751 Evaluate side-chains 48 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4722 GLN B 505 ASN B 509 GLN B 599 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.023823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.017645 restraints weight = 130654.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.018299 restraints weight = 84246.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.018791 restraints weight = 61419.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.019126 restraints weight = 48064.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019429 restraints weight = 40269.160| |-----------------------------------------------------------------------------| r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10675 Z= 0.252 Angle : 0.648 6.790 14491 Z= 0.340 Chirality : 0.041 0.142 1619 Planarity : 0.004 0.043 1858 Dihedral : 6.577 75.393 1469 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1301 helix: 1.41 (0.22), residues: 576 sheet: -0.21 (0.38), residues: 167 loop : 0.04 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A4745 TYR 0.021 0.002 TYR B 873 PHE 0.019 0.002 PHE B 711 TRP 0.010 0.002 TRP B 660 HIS 0.007 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00499 (10675) covalent geometry : angle 0.64819 (14491) hydrogen bonds : bond 0.04257 ( 509) hydrogen bonds : angle 5.67544 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.8152 (mmp) cc_final: 0.7715 (mmm) REVERT: A 4609 MET cc_start: 0.9654 (tpt) cc_final: 0.9209 (tpt) REVERT: A 4688 PHE cc_start: 0.9553 (t80) cc_final: 0.9144 (t80) REVERT: A 4692 LEU cc_start: 0.9760 (mt) cc_final: 0.9441 (mt) REVERT: B 69 MET cc_start: 0.8812 (mmm) cc_final: 0.8455 (mmp) REVERT: B 195 LEU cc_start: 0.9525 (tp) cc_final: 0.9286 (tt) REVERT: B 271 PHE cc_start: 0.9747 (p90) cc_final: 0.9101 (p90) REVERT: B 910 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9288 (mp) REVERT: B 1009 MET cc_start: 0.9226 (mmp) cc_final: 0.8791 (mmm) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0940 time to fit residues: 7.0751 Evaluate side-chains 38 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4792 HIS ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2301 r_free = 0.2301 target = 0.017168 restraints weight = 131864.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.017856 restraints weight = 84311.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.018366 restraints weight = 60885.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.018746 restraints weight = 47444.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019027 restraints weight = 39059.126| |-----------------------------------------------------------------------------| r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10675 Z= 0.181 Angle : 0.564 5.814 14491 Z= 0.299 Chirality : 0.040 0.143 1619 Planarity : 0.004 0.045 1858 Dihedral : 6.457 69.157 1469 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1301 helix: 1.43 (0.22), residues: 583 sheet: -0.43 (0.38), residues: 167 loop : -0.02 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4600 TYR 0.014 0.002 TYR A4528 PHE 0.017 0.002 PHE B 298 TRP 0.008 0.001 TRP B 660 HIS 0.004 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00364 (10675) covalent geometry : angle 0.56408 (14491) hydrogen bonds : bond 0.03955 ( 509) hydrogen bonds : angle 5.37571 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7997 (mmp) cc_final: 0.7664 (mmm) REVERT: A 4598 PHE cc_start: 0.9566 (m-80) cc_final: 0.8895 (m-80) REVERT: A 4613 ILE cc_start: 0.9633 (mm) cc_final: 0.9379 (tp) REVERT: A 4628 PHE cc_start: 0.9209 (m-80) cc_final: 0.8953 (m-80) REVERT: A 4688 PHE cc_start: 0.9549 (t80) cc_final: 0.9164 (t80) REVERT: A 4692 LEU cc_start: 0.9775 (mt) cc_final: 0.9470 (mt) REVERT: A 4740 MET cc_start: 0.9609 (mtt) cc_final: 0.9227 (mpp) REVERT: B 69 MET cc_start: 0.8703 (mmm) cc_final: 0.8341 (mmp) REVERT: B 195 LEU cc_start: 0.9508 (tp) cc_final: 0.9290 (tt) REVERT: B 271 PHE cc_start: 0.9796 (p90) cc_final: 0.9177 (p90) REVERT: B 909 MET cc_start: 0.9753 (tmm) cc_final: 0.9553 (tmm) REVERT: B 910 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9273 (mp) REVERT: B 1009 MET cc_start: 0.9275 (mmp) cc_final: 0.8962 (mmm) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0917 time to fit residues: 7.5897 Evaluate side-chains 41 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4758 HIS B 167 GLN B 518 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS B 760 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.023834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.017633 restraints weight = 131974.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.018300 restraints weight = 84725.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.018793 restraints weight = 61568.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.019166 restraints weight = 48279.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.019427 restraints weight = 39855.476| |-----------------------------------------------------------------------------| r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10675 Z= 0.245 Angle : 0.630 7.534 14491 Z= 0.330 Chirality : 0.041 0.174 1619 Planarity : 0.004 0.042 1858 Dihedral : 6.563 67.866 1469 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1301 helix: 1.18 (0.22), residues: 583 sheet: -0.58 (0.38), residues: 167 loop : -0.02 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4732 TYR 0.026 0.002 TYR A4528 PHE 0.017 0.002 PHE B 711 TRP 0.009 0.002 TRP B 660 HIS 0.006 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00485 (10675) covalent geometry : angle 0.63021 (14491) hydrogen bonds : bond 0.03964 ( 509) hydrogen bonds : angle 5.44031 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.8106 (mmp) cc_final: 0.7641 (mmm) REVERT: A 4609 MET cc_start: 0.9742 (tpt) cc_final: 0.9200 (tpt) REVERT: A 4688 PHE cc_start: 0.9561 (t80) cc_final: 0.9206 (t80) REVERT: A 4740 MET cc_start: 0.9651 (mtt) cc_final: 0.9341 (mpp) REVERT: B 69 MET cc_start: 0.8824 (mmm) cc_final: 0.8604 (mmm) REVERT: B 909 MET cc_start: 0.9784 (tmm) cc_final: 0.9575 (tmm) REVERT: B 910 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9255 (mp) REVERT: B 1009 MET cc_start: 0.9379 (mmp) cc_final: 0.9067 (mmm) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0937 time to fit residues: 6.7773 Evaluate side-chains 37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4707 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.018021 restraints weight = 125572.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.018707 restraints weight = 80818.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.019222 restraints weight = 58282.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.019610 restraints weight = 45588.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.019888 restraints weight = 37470.732| |-----------------------------------------------------------------------------| r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10675 Z= 0.136 Angle : 0.528 5.688 14491 Z= 0.277 Chirality : 0.040 0.179 1619 Planarity : 0.004 0.042 1858 Dihedral : 6.309 68.153 1469 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1301 helix: 1.47 (0.22), residues: 583 sheet: -0.51 (0.38), residues: 165 loop : -0.01 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4732 TYR 0.019 0.001 TYR A4528 PHE 0.014 0.001 PHE B 711 TRP 0.007 0.001 TRP A4738 HIS 0.003 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00277 (10675) covalent geometry : angle 0.52838 (14491) hydrogen bonds : bond 0.03569 ( 509) hydrogen bonds : angle 5.11721 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7927 (mmp) cc_final: 0.7511 (mmm) REVERT: A 4598 PHE cc_start: 0.9566 (m-80) cc_final: 0.8908 (m-80) REVERT: A 4609 MET cc_start: 0.9715 (tpt) cc_final: 0.9487 (tpp) REVERT: A 4613 ILE cc_start: 0.9642 (mm) cc_final: 0.9222 (tp) REVERT: A 4688 PHE cc_start: 0.9557 (t80) cc_final: 0.9172 (t80) REVERT: A 4692 LEU cc_start: 0.9785 (mt) cc_final: 0.9494 (mt) REVERT: A 4740 MET cc_start: 0.9660 (mtt) cc_final: 0.9313 (mpp) REVERT: B 69 MET cc_start: 0.8679 (mmm) cc_final: 0.8311 (mmp) REVERT: B 195 LEU cc_start: 0.9446 (tp) cc_final: 0.9236 (tt) REVERT: B 271 PHE cc_start: 0.9790 (p90) cc_final: 0.9153 (p90) REVERT: B 643 ASP cc_start: 0.9552 (m-30) cc_final: 0.9342 (m-30) REVERT: B 909 MET cc_start: 0.9773 (tmm) cc_final: 0.9556 (tmm) REVERT: B 910 ILE cc_start: 0.9579 (mp) cc_final: 0.9202 (mp) REVERT: B 1009 MET cc_start: 0.9306 (mmp) cc_final: 0.9014 (mmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0892 time to fit residues: 7.3841 Evaluate side-chains 41 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 56 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** 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 = 0.2633 r_free = 0.2633 target = 0.024391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.017995 restraints weight = 124996.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.018674 restraints weight = 80459.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019190 restraints weight = 58457.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.019571 restraints weight = 45722.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.019856 restraints weight = 37694.376| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10675 Z= 0.142 Angle : 0.524 5.750 14491 Z= 0.274 Chirality : 0.039 0.159 1619 Planarity : 0.004 0.041 1858 Dihedral : 6.180 69.442 1469 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1301 helix: 1.53 (0.22), residues: 584 sheet: -0.55 (0.38), residues: 165 loop : -0.01 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 809 TYR 0.020 0.001 TYR A4528 PHE 0.017 0.001 PHE B 711 TRP 0.006 0.001 TRP A4738 HIS 0.005 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00294 (10675) covalent geometry : angle 0.52438 (14491) hydrogen bonds : bond 0.03445 ( 509) hydrogen bonds : angle 5.07271 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7681 (mmp) cc_final: 0.7314 (mmm) REVERT: A 4598 PHE cc_start: 0.9585 (m-80) cc_final: 0.8949 (m-80) REVERT: A 4609 MET cc_start: 0.9706 (tpt) cc_final: 0.9486 (tpp) REVERT: A 4613 ILE cc_start: 0.9662 (mm) cc_final: 0.9267 (tp) REVERT: A 4688 PHE cc_start: 0.9565 (t80) cc_final: 0.9165 (t80) REVERT: A 4692 LEU cc_start: 0.9783 (mt) cc_final: 0.9495 (mt) REVERT: A 4740 MET cc_start: 0.9698 (mtt) cc_final: 0.9312 (mpp) REVERT: B 69 MET cc_start: 0.8648 (mmm) cc_final: 0.8340 (mmp) REVERT: B 271 PHE cc_start: 0.9791 (p90) cc_final: 0.9157 (p90) REVERT: B 643 ASP cc_start: 0.9550 (m-30) cc_final: 0.9347 (m-30) REVERT: B 909 MET cc_start: 0.9777 (tmm) cc_final: 0.9556 (tmm) REVERT: B 910 ILE cc_start: 0.9565 (mp) cc_final: 0.9167 (mp) REVERT: B 1009 MET cc_start: 0.9372 (mmp) cc_final: 0.9083 (mmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0820 time to fit residues: 6.6214 Evaluate side-chains 40 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** 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 = 0.2635 r_free = 0.2635 target = 0.024343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.018010 restraints weight = 125915.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.018694 restraints weight = 80783.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.019205 restraints weight = 58551.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.019599 restraints weight = 45761.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.019865 restraints weight = 37667.193| |-----------------------------------------------------------------------------| r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10675 Z= 0.136 Angle : 0.521 5.915 14491 Z= 0.272 Chirality : 0.039 0.141 1619 Planarity : 0.004 0.041 1858 Dihedral : 6.067 69.478 1469 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1301 helix: 1.65 (0.22), residues: 581 sheet: -0.51 (0.38), residues: 163 loop : -0.05 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4676 TYR 0.019 0.001 TYR A4528 PHE 0.015 0.001 PHE A4553 TRP 0.007 0.001 TRP A4738 HIS 0.003 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00281 (10675) covalent geometry : angle 0.52052 (14491) hydrogen bonds : bond 0.03371 ( 509) hydrogen bonds : angle 4.97823 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7741 (mmp) cc_final: 0.7403 (mmm) REVERT: A 4598 PHE cc_start: 0.9563 (m-80) cc_final: 0.8936 (m-80) REVERT: A 4609 MET cc_start: 0.9690 (tpt) cc_final: 0.9477 (tpp) REVERT: A 4613 ILE cc_start: 0.9656 (mm) cc_final: 0.9276 (tp) REVERT: A 4688 PHE cc_start: 0.9568 (t80) cc_final: 0.9151 (t80) REVERT: A 4692 LEU cc_start: 0.9783 (mt) cc_final: 0.9493 (mt) REVERT: A 4740 MET cc_start: 0.9701 (mtt) cc_final: 0.9379 (mpp) REVERT: B 69 MET cc_start: 0.8746 (mmm) cc_final: 0.8505 (mmm) REVERT: B 271 PHE cc_start: 0.9798 (p90) cc_final: 0.9160 (p90) REVERT: B 643 ASP cc_start: 0.9552 (m-30) cc_final: 0.9351 (m-30) REVERT: B 1009 MET cc_start: 0.9379 (mmp) cc_final: 0.9108 (mmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0848 time to fit residues: 6.6351 Evaluate side-chains 39 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** 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 = 0.2644 r_free = 0.2644 target = 0.024363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.018075 restraints weight = 125532.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.018763 restraints weight = 80430.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.019275 restraints weight = 57954.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.019649 restraints weight = 45069.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.019938 restraints weight = 37199.673| |-----------------------------------------------------------------------------| r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10675 Z= 0.117 Angle : 0.511 7.411 14491 Z= 0.265 Chirality : 0.039 0.140 1619 Planarity : 0.004 0.041 1858 Dihedral : 5.950 69.853 1469 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1301 helix: 1.68 (0.22), residues: 582 sheet: -0.49 (0.38), residues: 163 loop : -0.02 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4676 TYR 0.019 0.001 TYR A4528 PHE 0.014 0.001 PHE B 244 TRP 0.006 0.001 TRP A4738 HIS 0.003 0.001 HIS A4651 Details of bonding type rmsd covalent geometry : bond 0.00244 (10675) covalent geometry : angle 0.51129 (14491) hydrogen bonds : bond 0.03279 ( 509) hydrogen bonds : angle 4.87096 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7703 (mmp) cc_final: 0.7380 (mmm) REVERT: A 4598 PHE cc_start: 0.9572 (m-80) cc_final: 0.8956 (m-80) REVERT: A 4609 MET cc_start: 0.9657 (tpt) cc_final: 0.9451 (tpp) REVERT: A 4613 ILE cc_start: 0.9658 (mm) cc_final: 0.9294 (tp) REVERT: A 4688 PHE cc_start: 0.9561 (t80) cc_final: 0.9128 (t80) REVERT: A 4692 LEU cc_start: 0.9777 (mt) cc_final: 0.9499 (mt) REVERT: A 4740 MET cc_start: 0.9718 (mtt) cc_final: 0.9357 (mpp) REVERT: B 56 MET cc_start: 0.9563 (mpp) cc_final: 0.9218 (mpp) REVERT: B 69 MET cc_start: 0.8702 (mmm) cc_final: 0.8475 (mmm) REVERT: B 271 PHE cc_start: 0.9799 (p90) cc_final: 0.9153 (p90) REVERT: B 475 MET cc_start: 0.9240 (mmm) cc_final: 0.8942 (mmm) REVERT: B 909 MET cc_start: 0.9747 (tmm) cc_final: 0.9539 (tmm) REVERT: B 1009 MET cc_start: 0.9387 (mmp) cc_final: 0.9133 (mmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1011 time to fit residues: 8.2829 Evaluate side-chains 38 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.024847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.018387 restraints weight = 121045.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.019080 restraints weight = 78390.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.019590 restraints weight = 56884.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.019989 restraints weight = 44536.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.020277 restraints weight = 36693.265| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10675 Z= 0.092 Angle : 0.506 6.283 14491 Z= 0.259 Chirality : 0.040 0.134 1619 Planarity : 0.004 0.041 1858 Dihedral : 5.805 70.677 1469 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1301 helix: 1.75 (0.22), residues: 582 sheet: -0.33 (0.38), residues: 163 loop : -0.04 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4676 TYR 0.019 0.001 TYR A4528 PHE 0.017 0.001 PHE B 244 TRP 0.007 0.001 TRP A4738 HIS 0.003 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00192 (10675) covalent geometry : angle 0.50614 (14491) hydrogen bonds : bond 0.03183 ( 509) hydrogen bonds : angle 4.72260 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7550 (mmp) cc_final: 0.7255 (mmm) REVERT: A 4598 PHE cc_start: 0.9557 (m-80) cc_final: 0.8987 (m-80) REVERT: A 4740 MET cc_start: 0.9709 (mtt) cc_final: 0.9381 (mpp) REVERT: B 69 MET cc_start: 0.8816 (mmm) cc_final: 0.8461 (mmp) REVERT: B 271 PHE cc_start: 0.9799 (p90) cc_final: 0.9131 (p90) REVERT: B 475 MET cc_start: 0.9222 (mmm) cc_final: 0.8936 (mmm) REVERT: B 643 ASP cc_start: 0.9593 (m-30) cc_final: 0.9352 (m-30) REVERT: B 1009 MET cc_start: 0.9294 (mmp) cc_final: 0.9012 (mmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0867 time to fit residues: 7.2634 Evaluate side-chains 40 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.024872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.018381 restraints weight = 119317.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.019075 restraints weight = 77478.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.019580 restraints weight = 56504.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.019971 restraints weight = 44412.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.020251 restraints weight = 36755.587| |-----------------------------------------------------------------------------| r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10675 Z= 0.093 Angle : 0.499 6.413 14491 Z= 0.255 Chirality : 0.040 0.147 1619 Planarity : 0.004 0.040 1858 Dihedral : 5.703 71.400 1469 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1301 helix: 1.73 (0.22), residues: 582 sheet: -0.04 (0.37), residues: 170 loop : -0.09 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4676 TYR 0.019 0.001 TYR A4528 PHE 0.027 0.001 PHE A4632 TRP 0.005 0.001 TRP A4673 HIS 0.003 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00198 (10675) covalent geometry : angle 0.49887 (14491) hydrogen bonds : bond 0.03137 ( 509) hydrogen bonds : angle 4.68852 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.7543 (mmp) cc_final: 0.7251 (mmm) REVERT: A 4598 PHE cc_start: 0.9564 (m-80) cc_final: 0.9022 (m-80) REVERT: A 4609 MET cc_start: 0.9777 (tpt) cc_final: 0.9414 (tpp) REVERT: A 4740 MET cc_start: 0.9715 (mtt) cc_final: 0.9404 (mpp) REVERT: B 56 MET cc_start: 0.9551 (mpp) cc_final: 0.9133 (mpp) REVERT: B 69 MET cc_start: 0.8823 (mmm) cc_final: 0.8492 (mmp) REVERT: B 271 PHE cc_start: 0.9795 (p90) cc_final: 0.9107 (p90) REVERT: B 475 MET cc_start: 0.9223 (mmm) cc_final: 0.8944 (mmm) REVERT: B 643 ASP cc_start: 0.9585 (m-30) cc_final: 0.9355 (m-30) REVERT: B 1009 MET cc_start: 0.9315 (mmp) cc_final: 0.9033 (mmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0905 time to fit residues: 7.1887 Evaluate side-chains 41 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.024776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.018340 restraints weight = 121845.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.019030 restraints weight = 78945.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.019537 restraints weight = 57314.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.019931 restraints weight = 44964.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.020212 restraints weight = 37155.201| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10675 Z= 0.098 Angle : 0.492 6.233 14491 Z= 0.252 Chirality : 0.039 0.204 1619 Planarity : 0.004 0.040 1858 Dihedral : 5.632 71.716 1469 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1301 helix: 1.81 (0.22), residues: 580 sheet: -0.09 (0.37), residues: 172 loop : -0.06 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4676 TYR 0.019 0.001 TYR A4528 PHE 0.018 0.001 PHE B 244 TRP 0.006 0.001 TRP A4738 HIS 0.003 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00214 (10675) covalent geometry : angle 0.49187 (14491) hydrogen bonds : bond 0.03121 ( 509) hydrogen bonds : angle 4.64425 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.29 seconds wall clock time: 26 minutes 53.24 seconds (1613.24 seconds total)