Starting phenix.real_space_refine on Thu Mar 5 23:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mis_23863/03_2026/7mis_23863.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 9 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 46 5.16 5 Na 1 4.78 5 C 8258 2.51 5 N 2210 2.21 5 O 2517 1.98 5 H 12854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "C GLU 857": not complete - not flipped Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25893 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 12185 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 31, 'TRANS': 717} Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2047 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Chain: "C" Number of atoms: 11603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 11603 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 40, 'TRANS': 693} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' NA': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.18 Number of scatterers: 25893 At special positions: 0 Unit cell: (139.32, 138.24, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Ca 1 19.99 S 46 16.00 P 4 15.00 Mg 2 11.99 Na 1 11.00 O 2517 8.00 N 2210 7.00 C 8258 6.00 H 12854 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 838.6 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 11 sheets defined 60.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 135 through 158 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 184 through 206 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.717A pdb=" N MET A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.016A pdb=" N HIS A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.643A pdb=" N LEU A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.940A pdb=" N LYS A 328 " --> pdb=" O HIS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 4.134A pdb=" N LEU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 459 through 481 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 4.091A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.885A pdb=" N PHE A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.812A pdb=" N ARG A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 624 removed outlier: 3.817A pdb=" N TYR A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 655 removed outlier: 3.550A pdb=" N TRP A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 669 removed outlier: 3.725A pdb=" N ARG A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 684 through 689 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.766A pdb=" N SER A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 775 removed outlier: 3.586A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 794 Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 822 through 845 removed outlier: 4.387A pdb=" N SER A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.754A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.831A pdb=" N ALA B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.997A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.649A pdb=" N PHE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 Processing helix chain 'C' and resid 283 through 308 removed outlier: 3.598A pdb=" N THR C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.614A pdb=" N LYS C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 406 through 421 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 426 through 443 removed outlier: 3.959A pdb=" N THR C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 461 Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.534A pdb=" N ASP C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 505 " --> pdb=" O LYS C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 530 through 537 Processing helix chain 'C' and resid 553 through 561 removed outlier: 3.748A pdb=" N GLY C 557 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 584 removed outlier: 3.684A pdb=" N CYS C 566 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 578 " --> pdb=" O ARG C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 614 removed outlier: 3.572A pdb=" N ILE C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 603 " --> pdb=" O MET C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 631 through 642 Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 653 through 666 removed outlier: 3.845A pdb=" N LYS C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 661 " --> pdb=" O LYS C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 690 Processing helix chain 'C' and resid 697 through 711 removed outlier: 3.963A pdb=" N HIS C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 724 removed outlier: 4.111A pdb=" N ARG C 718 " --> pdb=" O TRP C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 753 Proline residue: C 743 - end of helix Processing helix chain 'C' and resid 768 through 784 Processing helix chain 'C' and resid 794 through 805 Processing helix chain 'C' and resid 807 through 812 removed outlier: 3.752A pdb=" N MET C 810 " --> pdb=" O PHE C 807 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 811 " --> pdb=" O SER C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 828 removed outlier: 3.906A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 910 through 929 Processing helix chain 'C' and resid 1056 through 1069 removed outlier: 4.563A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C1062 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP C1065 " --> pdb=" O GLY C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1077 through 1084 removed outlier: 3.977A pdb=" N ALA C1081 " --> pdb=" O ASN C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1111 Processing helix chain 'C' and resid 1126 through 1137 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.641A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS A 444 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 483 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 493 removed outlier: 4.059A pdb=" N ARG C 520 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 623 through 625 Processing sheet with id=AA9, first strand: chain 'C' and resid 669 through 670 removed outlier: 3.601A pdb=" N VAL C 681 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 760 through 765 removed outlier: 6.485A pdb=" N ILE C 834 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 892 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 836 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA C 894 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU C 838 " --> pdb=" O ALA C 894 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LYS C 896 " --> pdb=" O LEU C 838 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG C 887 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 877 " --> pdb=" O ARG C 887 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 889 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 875 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 891 " --> pdb=" O THR C 873 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 816 through 819 684 hydrogen bonds defined for protein. 1968 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: 6.07 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12844 1.03 - 1.23: 12 1.23 - 1.42: 5523 1.42 - 1.61: 7697 1.61 - 1.81: 82 Bond restraints: 26158 Sorted by residual: bond pdb=" C4 AMP C2000 " pdb=" C5 AMP C2000 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 AMP C2000 " pdb=" C6 AMP C2000 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O5' ATP A1001 " pdb=" PA ATP A1001 " ideal model delta sigma weight residual 1.579 1.611 -0.032 1.10e-02 8.26e+03 8.34e+00 bond pdb=" C8 AMP C2000 " pdb=" N7 AMP C2000 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 AMP C2000 " pdb=" N7 AMP C2000 " ideal model delta sigma weight residual 1.350 1.389 -0.039 2.00e-02 2.50e+03 3.74e+00 ... (remaining 26153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 47230 2.56 - 5.12: 93 5.12 - 7.68: 6 7.68 - 10.23: 4 10.23 - 12.79: 1 Bond angle restraints: 47334 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 132.44 7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 131.87 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" O1P AMP C2000 " pdb=" P AMP C2000 " pdb=" O3P AMP C2000 " ideal model delta sigma weight residual 119.90 107.11 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C1' AMP C2000 " pdb=" C2' AMP C2000 " pdb=" C3' AMP C2000 " ideal model delta sigma weight residual 111.00 101.26 9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N1 AMP C2000 " pdb=" C2 AMP C2000 " pdb=" N3 AMP C2000 " ideal model delta sigma weight residual 120.00 128.76 -8.76 3.00e+00 1.11e-01 8.53e+00 ... (remaining 47329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.33: 11838 28.33 - 56.66: 432 56.66 - 84.99: 44 84.99 - 113.32: 4 113.32 - 141.65: 1 Dihedral angle restraints: 12319 sinusoidal: 6755 harmonic: 5564 Sorted by residual: dihedral pdb=" C5' AMP C2000 " pdb=" O5' AMP C2000 " pdb=" P AMP C2000 " pdb=" O3P AMP C2000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.31 109.31 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" CA LEU C 544 " pdb=" C LEU C 544 " pdb=" N GLU C 545 " pdb=" CA GLU C 545 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CB GLU C 857 " pdb=" CG GLU C 857 " pdb=" CD GLU C 857 " pdb=" OE1 GLU C 857 " ideal model delta sinusoidal sigma weight residual 0.00 -141.65 141.65 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 12316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1619 0.045 - 0.090: 289 0.090 - 0.136: 68 0.136 - 0.181: 3 0.181 - 0.226: 1 Chirality restraints: 1980 Sorted by residual: chirality pdb=" C3' AMP C2000 " pdb=" C2' AMP C2000 " pdb=" C4' AMP C2000 " pdb=" O3' AMP C2000 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE C 901 " pdb=" N ILE C 901 " pdb=" C ILE C 901 " pdb=" CB ILE C 901 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1977 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AMP C2000 " -0.104 2.00e-02 2.50e+03 4.43e-02 5.39e+01 pdb=" C2 AMP C2000 " 0.014 2.00e-02 2.50e+03 pdb=" C4 AMP C2000 " 0.034 2.00e-02 2.50e+03 pdb=" C5 AMP C2000 " 0.025 2.00e-02 2.50e+03 pdb=" C6 AMP C2000 " -0.009 2.00e-02 2.50e+03 pdb=" C8 AMP C2000 " 0.032 2.00e-02 2.50e+03 pdb=" N1 AMP C2000 " -0.012 2.00e-02 2.50e+03 pdb=" N3 AMP C2000 " 0.037 2.00e-02 2.50e+03 pdb=" N6 AMP C2000 " -0.068 2.00e-02 2.50e+03 pdb=" N7 AMP C2000 " 0.031 2.00e-02 2.50e+03 pdb=" N9 AMP C2000 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 679 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO C 680 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 680 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 680 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1111 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C1112 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C1112 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C1112 " 0.027 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 863 2.16 - 2.77: 50250 2.77 - 3.38: 73169 3.38 - 3.99: 93107 3.99 - 4.60: 146618 Nonbonded interactions: 364007 Sorted by model distance: nonbonded pdb=" OD1 ASP C 697 " pdb=" H VAL C 698 " model vdw 1.552 2.450 nonbonded pdb="HE21 GLN B 50 " pdb=" OD1 ASN B 54 " model vdw 1.559 2.450 nonbonded pdb=" O TYR C 372 " pdb="HD22 ASN C 376 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU A 735 " pdb=" H GLU A 735 " model vdw 1.614 2.450 nonbonded pdb="HE22 GLN C 609 " pdb=" OD1 ASN C 652 " model vdw 1.615 2.450 ... (remaining 364002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.940 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: 0.150 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 0.108 13305 Z= 0.150 Angle : 0.518 12.793 17978 Z= 0.270 Chirality : 0.037 0.226 1980 Planarity : 0.004 0.073 2325 Dihedral : 14.717 141.649 5058 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1596 helix: 1.64 (0.18), residues: 850 sheet: 0.67 (0.53), residues: 99 loop : -0.82 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.020 0.001 TYR B 139 PHE 0.020 0.001 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00316 (13304) covalent geometry : angle 0.51833 (17978) hydrogen bonds : bond 0.12807 ( 684) hydrogen bonds : angle 5.24298 ( 1968) Misc. bond : bond 0.03615 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.686 Fit side-chains REVERT: A 425 PHE cc_start: 0.8416 (t80) cc_final: 0.8140 (t80) REVERT: A 821 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7529 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6942 (tp) cc_final: 0.6491 (tm) REVERT: B 52 MET cc_start: 0.6964 (mtm) cc_final: 0.6276 (ptm) REVERT: B 75 ARG cc_start: 0.6776 (tmm160) cc_final: 0.6553 (ttp-110) REVERT: B 84 GLU cc_start: 0.7142 (pm20) cc_final: 0.6848 (pm20) REVERT: B 138 ASN cc_start: 0.5977 (m110) cc_final: 0.5695 (t0) REVERT: C 291 MET cc_start: 0.8919 (mtp) cc_final: 0.8607 (mtp) REVERT: C 741 MET cc_start: 0.8369 (mmt) cc_final: 0.8121 (mmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.5409 time to fit residues: 268.9358 Evaluate side-chains 111 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS C 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097782 restraints weight = 54200.253| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.90 r_work: 0.3072 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13305 Z= 0.164 Angle : 0.530 6.993 17978 Z= 0.282 Chirality : 0.039 0.153 1980 Planarity : 0.004 0.049 2325 Dihedral : 6.076 77.402 1784 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.70 % Allowed : 6.31 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1596 helix: 1.36 (0.18), residues: 879 sheet: 0.56 (0.52), residues: 99 loop : -0.87 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 690 TYR 0.010 0.001 TYR C 256 PHE 0.023 0.001 PHE C 716 TRP 0.015 0.002 TRP A 845 HIS 0.009 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00376 (13304) covalent geometry : angle 0.52995 (17978) hydrogen bonds : bond 0.05549 ( 684) hydrogen bonds : angle 4.52039 ( 1968) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.683 Fit side-chains REVERT: A 425 PHE cc_start: 0.8524 (t80) cc_final: 0.8289 (t80) REVERT: A 427 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.7193 (ttt-90) REVERT: A 821 PRO cc_start: 0.7877 (Cg_endo) cc_final: 0.7594 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6865 (tp) cc_final: 0.6322 (tm) REVERT: B 52 MET cc_start: 0.7023 (mtm) cc_final: 0.6218 (ptm) REVERT: B 84 GLU cc_start: 0.7341 (pm20) cc_final: 0.7054 (pm20) REVERT: B 138 ASN cc_start: 0.5902 (m110) cc_final: 0.5584 (t0) REVERT: C 246 TYR cc_start: 0.6598 (t80) cc_final: 0.5915 (t80) REVERT: C 291 MET cc_start: 0.8934 (mtp) cc_final: 0.8628 (mtp) REVERT: C 632 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: C 1078 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3474 (pttt) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 1.4727 time to fit residues: 197.1388 Evaluate side-chains 118 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS C 609 GLN C 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098328 restraints weight = 54233.306| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.03 r_work: 0.3055 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13305 Z= 0.181 Angle : 0.528 6.880 17978 Z= 0.279 Chirality : 0.039 0.160 1980 Planarity : 0.004 0.041 2325 Dihedral : 6.000 71.663 1784 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.56 % Allowed : 8.20 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1596 helix: 1.33 (0.18), residues: 878 sheet: 0.40 (0.51), residues: 99 loop : -0.94 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 690 TYR 0.010 0.002 TYR C 256 PHE 0.024 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00427 (13304) covalent geometry : angle 0.52778 (17978) hydrogen bonds : bond 0.05535 ( 684) hydrogen bonds : angle 4.40861 ( 1968) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.742 Fit side-chains REVERT: A 821 PRO cc_start: 0.7878 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: B 75 ARG cc_start: 0.6879 (tmm160) cc_final: 0.6453 (tmm160) REVERT: B 84 GLU cc_start: 0.7366 (pm20) cc_final: 0.6171 (tp30) REVERT: B 138 ASN cc_start: 0.5822 (m110) cc_final: 0.5588 (t0) REVERT: C 291 MET cc_start: 0.8915 (mtp) cc_final: 0.8661 (mtp) REVERT: C 1078 LYS cc_start: 0.4364 (OUTLIER) cc_final: 0.3459 (pttt) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 1.5668 time to fit residues: 209.7050 Evaluate side-chains 118 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS C 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097769 restraints weight = 53778.929| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.89 r_work: 0.3074 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13305 Z= 0.136 Angle : 0.498 6.202 17978 Z= 0.262 Chirality : 0.038 0.139 1980 Planarity : 0.004 0.042 2325 Dihedral : 5.762 67.837 1784 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.63 % Allowed : 9.53 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1596 helix: 1.47 (0.18), residues: 876 sheet: 0.37 (0.51), residues: 99 loop : -0.91 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 427 TYR 0.009 0.001 TYR A 599 PHE 0.024 0.001 PHE C 716 TRP 0.005 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00312 (13304) covalent geometry : angle 0.49812 (17978) hydrogen bonds : bond 0.04933 ( 684) hydrogen bonds : angle 4.27380 ( 1968) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.796 Fit side-chains REVERT: A 205 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7469 (mppt) REVERT: B 75 ARG cc_start: 0.6850 (tmm160) cc_final: 0.6226 (ttp-170) REVERT: B 84 GLU cc_start: 0.7309 (pm20) cc_final: 0.6152 (tp30) REVERT: C 632 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: C 1078 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.3503 (pttt) outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 1.3834 time to fit residues: 187.2502 Evaluate side-chains 117 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096685 restraints weight = 54053.174| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.90 r_work: 0.3058 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13305 Z= 0.182 Angle : 0.528 6.754 17978 Z= 0.277 Chirality : 0.039 0.156 1980 Planarity : 0.004 0.047 2325 Dihedral : 5.819 67.930 1784 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 10.44 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1596 helix: 1.40 (0.18), residues: 878 sheet: 0.32 (0.51), residues: 99 loop : -0.97 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 427 TYR 0.009 0.002 TYR A 571 PHE 0.024 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00431 (13304) covalent geometry : angle 0.52787 (17978) hydrogen bonds : bond 0.05280 ( 684) hydrogen bonds : angle 4.30187 ( 1968) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.644 Fit side-chains REVERT: A 205 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7427 (mppt) REVERT: A 675 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8370 (t80) REVERT: B 84 GLU cc_start: 0.7352 (pm20) cc_final: 0.6219 (tp30) REVERT: C 632 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 1078 LYS cc_start: 0.4411 (OUTLIER) cc_final: 0.3513 (pttt) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 1.5551 time to fit residues: 207.4993 Evaluate side-chains 120 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098855 restraints weight = 53832.694| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.89 r_work: 0.3091 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13305 Z= 0.109 Angle : 0.482 5.807 17978 Z= 0.251 Chirality : 0.037 0.140 1980 Planarity : 0.004 0.050 2325 Dihedral : 5.510 63.648 1784 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.84 % Allowed : 11.07 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1596 helix: 1.63 (0.18), residues: 882 sheet: 0.39 (0.51), residues: 99 loop : -0.90 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.009 0.001 TYR A 599 PHE 0.023 0.001 PHE C 716 TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00241 (13304) covalent geometry : angle 0.48152 (17978) hydrogen bonds : bond 0.04453 ( 684) hydrogen bonds : angle 4.13564 ( 1968) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.704 Fit side-chains REVERT: A 205 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7412 (mppt) REVERT: A 675 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 75 ARG cc_start: 0.6843 (tmm160) cc_final: 0.6196 (ttp-170) REVERT: B 84 GLU cc_start: 0.7099 (pm20) cc_final: 0.6035 (tp30) REVERT: C 632 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: C 1078 LYS cc_start: 0.4405 (OUTLIER) cc_final: 0.3501 (pttt) outliers start: 12 outliers final: 6 residues processed: 130 average time/residue: 1.5295 time to fit residues: 215.6657 Evaluate side-chains 121 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096512 restraints weight = 54099.463| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.14 r_work: 0.3032 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13305 Z= 0.205 Angle : 0.541 6.764 17978 Z= 0.285 Chirality : 0.040 0.152 1980 Planarity : 0.004 0.055 2325 Dihedral : 5.777 66.159 1784 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.98 % Allowed : 11.42 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1596 helix: 1.44 (0.18), residues: 883 sheet: 0.46 (0.50), residues: 104 loop : -1.01 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 427 TYR 0.010 0.002 TYR C 392 PHE 0.024 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00489 (13304) covalent geometry : angle 0.54092 (17978) hydrogen bonds : bond 0.05396 ( 684) hydrogen bonds : angle 4.27794 ( 1968) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 675 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8291 (t80) REVERT: B 84 GLU cc_start: 0.7198 (pm20) cc_final: 0.6167 (tp30) REVERT: C 632 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7904 (tt0) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 1.6013 time to fit residues: 217.7314 Evaluate side-chains 122 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099210 restraints weight = 53966.083| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.03 r_work: 0.3070 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13305 Z= 0.135 Angle : 0.500 6.065 17978 Z= 0.262 Chirality : 0.038 0.139 1980 Planarity : 0.004 0.053 2325 Dihedral : 5.600 64.141 1784 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.12 % Allowed : 11.91 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1596 helix: 1.56 (0.18), residues: 881 sheet: 0.33 (0.51), residues: 99 loop : -0.95 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.009 0.001 TYR A 274 PHE 0.023 0.001 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00311 (13304) covalent geometry : angle 0.50002 (17978) hydrogen bonds : bond 0.04801 ( 684) hydrogen bonds : angle 4.18074 ( 1968) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.716 Fit side-chains REVERT: A 205 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7418 (mppt) REVERT: A 675 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 84 GLU cc_start: 0.7058 (pm20) cc_final: 0.6037 (tp30) REVERT: C 632 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 1078 LYS cc_start: 0.4402 (OUTLIER) cc_final: 0.3498 (pttt) outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 1.5540 time to fit residues: 212.7392 Evaluate side-chains 125 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098923 restraints weight = 54084.794| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13305 Z= 0.135 Angle : 0.499 6.023 17978 Z= 0.261 Chirality : 0.038 0.140 1980 Planarity : 0.004 0.057 2325 Dihedral : 5.567 62.401 1784 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.91 % Allowed : 12.47 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1596 helix: 1.62 (0.18), residues: 881 sheet: 0.47 (0.50), residues: 104 loop : -0.96 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.008 0.001 TYR A 274 PHE 0.024 0.001 PHE C 716 TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00315 (13304) covalent geometry : angle 0.49917 (17978) hydrogen bonds : bond 0.04714 ( 684) hydrogen bonds : angle 4.14403 ( 1968) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.723 Fit side-chains REVERT: A 205 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7445 (mppt) REVERT: A 675 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8391 (t80) REVERT: B 84 GLU cc_start: 0.7048 (pm20) cc_final: 0.6042 (tp30) REVERT: C 632 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: C 1078 LYS cc_start: 0.4394 (OUTLIER) cc_final: 0.3511 (pttt) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 1.5492 time to fit residues: 214.7465 Evaluate side-chains 123 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 105 optimal weight: 0.0060 chunk 117 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099457 restraints weight = 53772.350| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.14 r_work: 0.3080 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13305 Z= 0.106 Angle : 0.480 5.778 17978 Z= 0.250 Chirality : 0.037 0.143 1980 Planarity : 0.004 0.098 2325 Dihedral : 5.382 59.890 1784 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.84 % Allowed : 12.68 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1596 helix: 1.77 (0.18), residues: 880 sheet: 0.51 (0.50), residues: 104 loop : -0.87 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 690 TYR 0.010 0.001 TYR C 246 PHE 0.023 0.001 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00236 (13304) covalent geometry : angle 0.47990 (17978) hydrogen bonds : bond 0.04202 ( 684) hydrogen bonds : angle 4.03485 ( 1968) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.732 Fit side-chains REVERT: A 205 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7404 (mppt) REVERT: A 675 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 84 GLU cc_start: 0.7013 (pm20) cc_final: 0.6045 (tp30) REVERT: C 1078 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.3488 (pttt) outliers start: 12 outliers final: 6 residues processed: 127 average time/residue: 1.6067 time to fit residues: 221.2439 Evaluate side-chains 122 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095395 restraints weight = 53930.147| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.89 r_work: 0.3036 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13305 Z= 0.270 Angle : 0.599 7.167 17978 Z= 0.316 Chirality : 0.043 0.207 1980 Planarity : 0.005 0.063 2325 Dihedral : 5.901 65.390 1784 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 0.84 % Allowed : 12.47 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1596 helix: 1.33 (0.17), residues: 885 sheet: 0.41 (0.50), residues: 104 loop : -1.08 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 522 TYR 0.023 0.002 TYR A 245 PHE 0.025 0.002 PHE C 716 TRP 0.011 0.002 TRP A 845 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00650 (13304) covalent geometry : angle 0.59871 (17978) hydrogen bonds : bond 0.05907 ( 684) hydrogen bonds : angle 4.35839 ( 1968) Misc. bond : bond 0.00127 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9381.33 seconds wall clock time: 159 minutes 6.58 seconds (9546.58 seconds total)