Starting phenix.real_space_refine on Mon Nov 13 23:46:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d10_30542/11_2023/7d10_30542_updated.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4294 2.51 5 N 1000 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 307": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6424 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3176 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.97, per 1000 atoms: 0.62 Number of scatterers: 6424 At special positions: 0 Unit cell: (101.463, 79.643, 88.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1102 8.00 N 1000 7.00 C 4294 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: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 60.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.789A pdb=" N ASN A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 320 through 341 removed outlier: 3.738A pdb=" N THR A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 362 through 388 removed outlier: 3.909A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.648A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.948A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 487 through 497 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.627A pdb=" N ILE A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 525 through 541 removed outlier: 3.606A pdb=" N LEU A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.783A pdb=" N ILE A 607 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.820A pdb=" N LYS A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.633A pdb=" N ILE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 698 Proline residue: A 676 - end of helix removed outlier: 4.348A pdb=" N PHE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.741A pdb=" N CYS A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 750 removed outlier: 3.735A pdb=" N LEU A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.789A pdb=" N ASN B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 320 through 341 removed outlier: 3.738A pdb=" N THR B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 357 No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 362 through 388 removed outlier: 3.908A pdb=" N ALA B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.647A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.948A pdb=" N ILE B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 487 through 497 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.627A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 525 through 541 removed outlier: 3.607A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.783A pdb=" N ILE B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.821A pdb=" N LYS B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.634A pdb=" N ILE B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Proline residue: B 676 - end of helix removed outlier: 4.349A pdb=" N PHE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 729 removed outlier: 3.741A pdb=" N CYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 727 " --> pdb=" O CYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 removed outlier: 3.735A pdb=" N LEU B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 746 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1592 1.33 - 1.45: 1190 1.45 - 1.57: 3718 1.57 - 1.68: 2 1.68 - 1.80: 46 Bond restraints: 6548 Sorted by residual: bond pdb=" C ALA A 622 " pdb=" N PRO A 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C ALA B 622 " pdb=" N PRO B 623 " ideal model delta sigma weight residual 1.337 1.373 -0.036 1.24e-02 6.50e+03 8.22e+00 bond pdb=" C PHE A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.337 1.359 -0.023 9.80e-03 1.04e+04 5.32e+00 bond pdb=" C PHE B 495 " pdb=" N PRO B 496 " ideal model delta sigma weight residual 1.337 1.359 -0.022 9.80e-03 1.04e+04 5.18e+00 bond pdb=" C ILE B 518 " pdb=" O ILE B 518 " ideal model delta sigma weight residual 1.240 1.216 0.024 1.22e-02 6.72e+03 3.88e+00 ... (remaining 6543 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.87: 104 105.87 - 112.93: 3443 112.93 - 119.99: 2632 119.99 - 127.05: 2688 127.05 - 134.12: 59 Bond angle restraints: 8926 Sorted by residual: angle pdb=" N PRO B 581 " pdb=" CA PRO B 581 " pdb=" CB PRO B 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.45e+01 angle pdb=" N PRO A 581 " pdb=" CA PRO A 581 " pdb=" CB PRO A 581 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.44e+01 angle pdb=" N ALA B 517 " pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 111.36 119.01 -7.65 1.09e+00 8.42e-01 4.93e+01 angle pdb=" N ALA A 517 " pdb=" CA ALA A 517 " pdb=" C ALA A 517 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N PRO A 754 " pdb=" CA PRO A 754 " pdb=" CB PRO A 754 " ideal model delta sigma weight residual 103.00 110.65 -7.65 1.10e+00 8.26e-01 4.84e+01 ... (remaining 8921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 3363 11.91 - 23.82: 278 23.82 - 35.73: 79 35.73 - 47.64: 25 47.64 - 59.55: 5 Dihedral angle restraints: 3750 sinusoidal: 1208 harmonic: 2542 Sorted by residual: dihedral pdb=" CA ALA B 707 " pdb=" C ALA B 707 " pdb=" N PHE B 708 " pdb=" CA PHE B 708 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 707 " pdb=" C ALA A 707 " pdb=" N PHE A 708 " pdb=" CA PHE A 708 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 3747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 777 0.058 - 0.116: 275 0.116 - 0.174: 52 0.174 - 0.232: 10 0.232 - 0.289: 4 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA LYS B 520 " pdb=" N LYS B 520 " pdb=" C LYS B 520 " pdb=" CB LYS B 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LYS A 520 " pdb=" N LYS A 520 " pdb=" C LYS A 520 " pdb=" CB LYS A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ALA B 517 " pdb=" N ALA B 517 " pdb=" C ALA B 517 " pdb=" CB ALA B 517 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1115 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 518 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO B 519 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 518 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 519 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 519 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 519 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 515 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLN B 515 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN B 515 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 516 " 0.024 2.00e-02 2.50e+03 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1606 2.78 - 3.31: 5842 3.31 - 3.84: 10101 3.84 - 4.37: 11984 4.37 - 4.90: 20201 Nonbonded interactions: 49734 Sorted by model distance: nonbonded pdb=" O LEU B 438 " pdb=" OG SER B 609 " model vdw 2.249 2.440 nonbonded pdb=" O LEU A 438 " pdb=" OG SER A 609 " model vdw 2.249 2.440 nonbonded pdb=" O SER A 339 " pdb=" OG1 THR A 343 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 339 " pdb=" OG1 THR B 343 " model vdw 2.295 2.440 nonbonded pdb=" O THR A 499 " pdb=" OH TYR A 686 " model vdw 2.341 2.440 ... (remaining 49729 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 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: 0.380 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: 1.930 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.880 Find NCS groups from input model: 0.370 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.007 0.063 6548 Z= 0.438 Angle : 1.055 10.800 8926 Z= 0.592 Chirality : 0.063 0.289 1118 Planarity : 0.009 0.116 1084 Dihedral : 10.873 59.548 2114 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.94 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % 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: -6.70 (0.15), residues: 872 helix: -4.28 (0.10), residues: 594 sheet: None (None), residues: 0 loop : -4.33 (0.25), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.702 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1671 time to fit residues: 33.9921 Evaluate side-chains 95 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 474 ASN A 476 ASN A 506 ASN B 298 ASN B 474 ASN B 476 ASN B 506 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6548 Z= 0.168 Angle : 0.554 6.069 8926 Z= 0.289 Chirality : 0.041 0.117 1118 Planarity : 0.005 0.064 1084 Dihedral : 7.570 57.933 974 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.71 % Allowed : 12.79 % Favored : 82.49 % 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: -4.83 (0.21), residues: 872 helix: -2.70 (0.17), residues: 586 sheet: None (None), residues: 0 loop : -4.01 (0.26), residues: 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.724 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 141 average time/residue: 0.1536 time to fit residues: 30.6302 Evaluate side-chains 127 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0594 time to fit residues: 2.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.225 Angle : 0.556 5.955 8926 Z= 0.288 Chirality : 0.042 0.128 1118 Planarity : 0.004 0.046 1084 Dihedral : 7.207 57.551 974 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.01 % Allowed : 17.85 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.24), residues: 872 helix: -2.02 (0.19), residues: 600 sheet: None (None), residues: 0 loop : -3.88 (0.28), residues: 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.694 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 118 average time/residue: 0.1681 time to fit residues: 27.1012 Evaluate side-chains 113 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0614 time to fit residues: 1.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6548 Z= 0.155 Angle : 0.514 6.971 8926 Z= 0.266 Chirality : 0.041 0.116 1118 Planarity : 0.004 0.040 1084 Dihedral : 6.697 59.190 974 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.19 % Allowed : 16.84 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.26), residues: 872 helix: -1.53 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.66 (0.30), residues: 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.703 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 0.1717 time to fit residues: 30.7968 Evaluate side-chains 123 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1226 time to fit residues: 2.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6548 Z= 0.228 Angle : 0.544 6.332 8926 Z= 0.283 Chirality : 0.043 0.128 1118 Planarity : 0.004 0.039 1084 Dihedral : 6.859 55.032 974 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 872 helix: -1.16 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -3.62 (0.29), residues: 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.731 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.1822 time to fit residues: 30.0491 Evaluate side-chains 121 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0931 time to fit residues: 2.2387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.211 Angle : 0.538 5.589 8926 Z= 0.278 Chirality : 0.042 0.124 1118 Planarity : 0.004 0.039 1084 Dihedral : 6.857 59.380 974 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.36 % Allowed : 19.53 % Favored : 78.11 % 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: -2.61 (0.27), residues: 872 helix: -0.86 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.709 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.1770 time to fit residues: 30.4130 Evaluate side-chains 119 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1009 time to fit residues: 2.3918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 506 ASN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6548 Z= 0.163 Angle : 0.519 7.883 8926 Z= 0.267 Chirality : 0.041 0.118 1118 Planarity : 0.004 0.039 1084 Dihedral : 6.454 55.907 974 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.35 % Allowed : 20.54 % Favored : 78.11 % 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: -2.36 (0.28), residues: 872 helix: -0.67 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.51 (0.32), residues: 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.723 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.1844 time to fit residues: 28.1361 Evaluate side-chains 109 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1245 time to fit residues: 1.8187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN A 515 GLN A 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6548 Z= 0.256 Angle : 0.564 7.245 8926 Z= 0.291 Chirality : 0.044 0.129 1118 Planarity : 0.004 0.037 1084 Dihedral : 6.609 56.654 974 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.18 % Allowed : 21.72 % Favored : 77.10 % 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: -2.32 (0.28), residues: 872 helix: -0.64 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.52 (0.32), residues: 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.707 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 107 average time/residue: 0.1921 time to fit residues: 27.3458 Evaluate side-chains 106 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1097 time to fit residues: 1.8906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6548 Z= 0.160 Angle : 0.520 7.485 8926 Z= 0.266 Chirality : 0.041 0.121 1118 Planarity : 0.004 0.038 1084 Dihedral : 6.041 53.423 974 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.17 % Allowed : 23.06 % Favored : 76.77 % 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: -2.00 (0.29), residues: 872 helix: -0.37 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.43 (0.33), residues: 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.640 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1755 time to fit residues: 26.6884 Evaluate side-chains 104 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3377 time to fit residues: 1.3454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.188 Angle : 0.536 7.431 8926 Z= 0.275 Chirality : 0.042 0.126 1118 Planarity : 0.004 0.037 1084 Dihedral : 6.001 53.005 974 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.51 % Allowed : 24.41 % Favored : 75.08 % 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: -1.88 (0.29), residues: 872 helix: -0.26 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.46 (0.33), residues: 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.691 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 105 average time/residue: 0.1940 time to fit residues: 27.0217 Evaluate side-chains 105 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1574 time to fit residues: 1.5171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 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 = 0.3539 r_free = 0.3539 target = 0.131267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.104868 restraints weight = 8634.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107791 restraints weight = 4818.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109423 restraints weight = 3494.288| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.180 Angle : 0.531 7.338 8926 Z= 0.272 Chirality : 0.042 0.126 1118 Planarity : 0.004 0.038 1084 Dihedral : 5.920 53.269 974 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.67 % Allowed : 24.58 % Favored : 74.75 % 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: -1.74 (0.29), residues: 872 helix: -0.15 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.44 (0.33), residues: 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.93 seconds wall clock time: 26 minutes 13.21 seconds (1573.21 seconds total)