Starting phenix.real_space_refine on Sun Dec 10 01:30:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x06_32918/12_2023/7x06_32918_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 8400 2.51 5 N 2156 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6456 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 1 Chain: "B" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6456 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.03, per 1000 atoms: 0.54 Number of scatterers: 12964 At special positions: 0 Unit cell: (114.49, 116.63, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 4 15.00 Mg 2 11.99 O 2330 8.00 N 2156 7.00 C 8400 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 - 3.50 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: 5.06 Conformation dependent library (CDL) restraints added in 2.3 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 4 sheets defined 59.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 113 through 132 removed outlier: 4.263A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 162 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 424 through 446 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 529 through 559 removed outlier: 5.458A pdb=" N GLY A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 586 Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.524A pdb=" N GLN A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 646 Processing helix chain 'A' and resid 653 through 680 Processing helix chain 'A' and resid 685 through 705 removed outlier: 5.191A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 735 removed outlier: 5.146A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 721 " --> pdb=" O HIS A 717 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 722 " --> pdb=" O TYR A 718 " (cutoff:3.500A) Proline residue: A 723 - end of helix Processing helix chain 'A' and resid 765 through 818 Processing helix chain 'A' and resid 825 through 856 removed outlier: 5.263A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 113 through 132 removed outlier: 4.263A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 162 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 243 through 262 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 424 through 446 Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 486 through 489 No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 529 through 559 removed outlier: 5.457A pdb=" N GLY B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR B 558 " --> pdb=" O TRP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 586 Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.524A pdb=" N GLN B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 646 Processing helix chain 'B' and resid 653 through 680 Processing helix chain 'B' and resid 685 through 705 removed outlier: 5.190A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 735 removed outlier: 5.146A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 720 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 721 " --> pdb=" O HIS B 717 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 722 " --> pdb=" O TYR B 718 " (cutoff:3.500A) Proline residue: B 723 - end of helix Processing helix chain 'B' and resid 765 through 818 Processing helix chain 'B' and resid 825 through 856 removed outlier: 5.263A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 177 through 180 removed outlier: 8.045A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 377 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N CYS A 235 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA A 379 " --> pdb=" O CYS A 235 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR A 237 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N MET A 381 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A 512 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 408 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 514 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY A 410 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 516 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 411 through 414 Processing sheet with id= C, first strand: chain 'B' and resid 177 through 180 removed outlier: 8.045A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR B 377 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N CYS B 235 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA B 379 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR B 237 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N MET B 381 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 512 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 408 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 514 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY B 410 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 516 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 411 through 414 748 hydrogen bonds defined for protein. 2214 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: 4.50 Time building geometry restraints manager: 5.46 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: 4075 1.34 - 1.46: 2257 1.46 - 1.57: 6862 1.57 - 1.69: 6 1.69 - 1.81: 112 Bond restraints: 13312 Sorted by residual: bond pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.00e-02 1.00e+04 1.54e+01 bond pdb=" C TYR B 462 " pdb=" N GLU B 463 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.33e+00 bond pdb=" C TYR A 462 " pdb=" N GLU A 463 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.23e+00 bond pdb=" C ASN B 541 " pdb=" O ASN B 541 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.15e-02 7.56e+03 1.17e+00 ... (remaining 13307 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.70: 375 106.70 - 113.53: 7151 113.53 - 120.36: 5164 120.36 - 127.19: 5232 127.19 - 134.02: 160 Bond angle restraints: 18082 Sorted by residual: angle pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 112.05 -9.10 1.00e+00 1.00e+00 8.28e+01 angle pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 102.95 112.01 -9.06 1.00e+00 1.00e+00 8.22e+01 angle pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3B UDP A1001 " ideal model delta sigma weight residual 112.01 103.00 9.01 1.00e+00 1.00e+00 8.11e+01 angle pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3B UDP B1001 " ideal model delta sigma weight residual 112.01 103.02 8.99 1.00e+00 1.00e+00 8.08e+01 angle pdb=" N CYS A 47 " pdb=" CA CYS A 47 " pdb=" C CYS A 47 " ideal model delta sigma weight residual 114.04 110.73 3.31 1.24e+00 6.50e-01 7.12e+00 ... (remaining 18077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 7293 16.48 - 32.96: 391 32.96 - 49.44: 56 49.44 - 65.92: 10 65.92 - 82.40: 4 Dihedral angle restraints: 7754 sinusoidal: 3044 harmonic: 4710 Sorted by residual: dihedral pdb=" CA GLY A 455 " pdb=" C GLY A 455 " pdb=" N ALA A 456 " pdb=" CA ALA A 456 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY B 455 " pdb=" C GLY B 455 " pdb=" N ALA B 456 " pdb=" CA ALA B 456 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1141 0.026 - 0.052: 541 0.052 - 0.078: 187 0.078 - 0.103: 78 0.103 - 0.129: 37 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 288 " pdb=" N ILE B 288 " pdb=" C ILE B 288 " pdb=" CB ILE B 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA PHE A 545 " pdb=" N PHE A 545 " pdb=" C PHE A 545 " pdb=" CB PHE A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1981 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C PHE B 598 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C PHE A 598 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ILE B 599 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.013 2.00e-02 2.50e+03 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1799 2.75 - 3.29: 11968 3.29 - 3.83: 21138 3.83 - 4.36: 23124 4.36 - 4.90: 43416 Nonbonded interactions: 101445 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 52 " model vdw 2.228 2.440 nonbonded pdb=" OE1 GLU A 312 " pdb=" NH2 ARG B 773 " model vdw 2.292 2.520 nonbonded pdb=" OG SER A 93 " pdb=" O LYS B 762 " model vdw 2.315 2.440 nonbonded pdb=" NH2 ARG A 773 " pdb=" OE1 GLU B 312 " model vdw 2.318 2.520 ... (remaining 101440 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.020 Extract box with map and model: 6.090 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.260 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 13312 Z= 0.191 Angle : 0.508 9.098 18082 Z= 0.297 Chirality : 0.038 0.129 1984 Planarity : 0.004 0.027 2282 Dihedral : 10.343 82.402 4730 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.43 % Allowed : 4.62 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.22), residues: 1600 helix: 2.76 (0.17), residues: 966 sheet: -0.19 (0.40), residues: 170 loop : -1.14 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.003 0.001 HIS B 709 PHE 0.012 0.001 PHE B 545 TYR 0.013 0.001 TYR B 473 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 222 average time/residue: 0.2876 time to fit residues: 89.6562 Evaluate side-chains 139 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1173 time to fit residues: 2.4196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 295 GLN B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13312 Z= 0.347 Angle : 0.581 9.308 18082 Z= 0.304 Chirality : 0.042 0.144 1984 Planarity : 0.004 0.032 2282 Dihedral : 4.277 24.395 1764 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.17 % Allowed : 8.67 % Favored : 89.16 % 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: 1.58 (0.21), residues: 1600 helix: 2.35 (0.16), residues: 962 sheet: -0.37 (0.40), residues: 172 loop : -1.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 804 HIS 0.005 0.001 HIS B 394 PHE 0.018 0.002 PHE A 545 TYR 0.031 0.002 TYR A 732 ARG 0.004 0.001 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.2317 time to fit residues: 60.7791 Evaluate side-chains 155 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1225 time to fit residues: 6.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 295 GLN B 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13312 Z= 0.205 Angle : 0.492 6.998 18082 Z= 0.260 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.153 23.018 1764 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.16 % Allowed : 10.84 % Favored : 88.01 % 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: 1.69 (0.22), residues: 1600 helix: 2.51 (0.17), residues: 958 sheet: -0.67 (0.41), residues: 158 loop : -1.17 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 804 HIS 0.004 0.001 HIS A 327 PHE 0.014 0.001 PHE B 545 TYR 0.028 0.001 TYR B 732 ARG 0.006 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.2364 time to fit residues: 53.7893 Evaluate side-chains 144 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1241 time to fit residues: 4.7021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN B 295 GLN B 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13312 Z= 0.212 Angle : 0.489 7.040 18082 Z= 0.258 Chirality : 0.038 0.134 1984 Planarity : 0.004 0.030 2282 Dihedral : 4.077 22.507 1764 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.08 % Allowed : 12.50 % Favored : 86.42 % 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: 1.72 (0.22), residues: 1600 helix: 2.49 (0.17), residues: 970 sheet: -0.81 (0.41), residues: 160 loop : -1.08 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 804 HIS 0.003 0.001 HIS A 394 PHE 0.014 0.001 PHE A 545 TYR 0.031 0.001 TYR B 732 ARG 0.007 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 143 average time/residue: 0.2473 time to fit residues: 52.9996 Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1223 time to fit residues: 4.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 13312 Z= 0.486 Angle : 0.634 8.728 18082 Z= 0.338 Chirality : 0.045 0.156 1984 Planarity : 0.005 0.040 2282 Dihedral : 4.513 23.299 1764 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.44 % Rotamer: Outliers : 1.01 % Allowed : 13.87 % Favored : 85.12 % 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: 1.09 (0.21), residues: 1600 helix: 2.01 (0.17), residues: 958 sheet: -0.47 (0.40), residues: 172 loop : -1.56 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 511 HIS 0.005 0.001 HIS A 394 PHE 0.020 0.002 PHE B 545 TYR 0.026 0.002 TYR A 732 ARG 0.007 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 150 average time/residue: 0.2297 time to fit residues: 52.8016 Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1394 time to fit residues: 3.7956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN B 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13312 Z= 0.190 Angle : 0.486 6.860 18082 Z= 0.258 Chirality : 0.038 0.132 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.185 22.759 1764 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.87 % Allowed : 14.74 % Favored : 84.39 % 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: 1.60 (0.22), residues: 1600 helix: 2.49 (0.17), residues: 946 sheet: -0.48 (0.40), residues: 176 loop : -1.35 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 511 HIS 0.002 0.001 HIS A 430 PHE 0.015 0.001 PHE B 545 TYR 0.021 0.001 TYR A 732 ARG 0.002 0.000 ARG B 797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 144 average time/residue: 0.2497 time to fit residues: 54.1007 Evaluate side-chains 145 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1279 time to fit residues: 4.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN B 318 ASN B 334 GLN B 736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13312 Z= 0.198 Angle : 0.487 7.061 18082 Z= 0.257 Chirality : 0.039 0.146 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.069 21.499 1764 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.87 % Allowed : 14.38 % Favored : 84.75 % 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: 1.69 (0.22), residues: 1600 helix: 2.57 (0.17), residues: 946 sheet: -0.47 (0.40), residues: 176 loop : -1.31 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 202 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE B 545 TYR 0.028 0.001 TYR B 732 ARG 0.004 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 146 average time/residue: 0.2516 time to fit residues: 55.1020 Evaluate side-chains 140 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1327 time to fit residues: 3.2498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 318 ASN B 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13312 Z= 0.172 Angle : 0.472 6.768 18082 Z= 0.249 Chirality : 0.038 0.164 1984 Planarity : 0.004 0.030 2282 Dihedral : 3.991 21.750 1764 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.87 % Allowed : 14.88 % Favored : 84.25 % 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: 1.73 (0.22), residues: 1600 helix: 2.52 (0.17), residues: 970 sheet: -0.70 (0.41), residues: 158 loop : -1.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 563 PHE 0.013 0.001 PHE B 601 TYR 0.024 0.001 TYR B 732 ARG 0.004 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.2493 time to fit residues: 52.3046 Evaluate side-chains 138 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1378 time to fit residues: 4.0897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13312 Z= 0.344 Angle : 0.557 10.882 18082 Z= 0.295 Chirality : 0.042 0.165 1984 Planarity : 0.004 0.030 2282 Dihedral : 4.226 21.727 1764 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 0.51 % Allowed : 14.88 % Favored : 84.61 % 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: 1.43 (0.22), residues: 1600 helix: 2.28 (0.17), residues: 960 sheet: -0.53 (0.40), residues: 176 loop : -1.37 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.003 0.001 HIS B 430 PHE 0.016 0.002 PHE A 545 TYR 0.028 0.002 TYR A 732 ARG 0.003 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 136 average time/residue: 0.2398 time to fit residues: 49.3185 Evaluate side-chains 136 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1423 time to fit residues: 2.8857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13312 Z= 0.188 Angle : 0.493 10.937 18082 Z= 0.259 Chirality : 0.038 0.134 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.088 21.939 1764 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.36 % Allowed : 15.03 % Favored : 84.61 % 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: 1.71 (0.22), residues: 1600 helix: 2.45 (0.17), residues: 970 sheet: -0.41 (0.41), residues: 176 loop : -1.22 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 511 HIS 0.002 0.001 HIS B 394 PHE 0.014 0.001 PHE B 545 TYR 0.026 0.001 TYR A 732 ARG 0.002 0.000 ARG A 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 138 average time/residue: 0.2574 time to fit residues: 52.8933 Evaluate side-chains 136 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1378 time to fit residues: 2.7640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.3499 r_free = 0.3499 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099151 restraints weight = 15602.552| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.25 r_work: 0.3070 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13312 Z= 0.283 Angle : 0.529 8.439 18082 Z= 0.280 Chirality : 0.040 0.145 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.169 21.666 1764 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.14 % Allowed : 15.17 % Favored : 84.68 % 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: 1.52 (0.22), residues: 1600 helix: 2.30 (0.17), residues: 972 sheet: -0.48 (0.40), residues: 176 loop : -1.28 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 511 HIS 0.003 0.001 HIS A 709 PHE 0.015 0.001 PHE A 545 TYR 0.026 0.001 TYR B 732 ARG 0.003 0.000 ARG A 231 =============================================================================== Job complete usr+sys time: 2667.15 seconds wall clock time: 49 minutes 48.95 seconds (2988.95 seconds total)