Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 23:09:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/04_2023/6jyl_9718_updated.pdb" } resolution = 3.37 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 ------------------------------------------------------------------------------- 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9259 2.51 5 N 2959 2.21 5 O 3594 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K ARG 308": "NH1" <-> "NH2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "K TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 614": "NH1" <-> "NH2" Residue "K ARG 639": "NH1" <-> "NH2" Residue "K ARG 645": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16136 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4161 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'peptide': 504, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 485, None: 3} Not linked: pdbres="SER K 657 " pdbres="ADP K1201 " Not linked: pdbres="ADP K1201 " pdbres="BEF K1202 " Not linked: pdbres="BEF K1202 " pdbres=" MG K1203 " Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.32, per 1000 atoms: 0.52 Number of scatterers: 16136 At special positions: 0 Unit cell: (146.59, 130.54, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3594 8.00 N 2959 7.00 C 9259 6.00 Be 1 4.00 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: 7.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 3 sheets defined 55.9% alpha, 2.5% beta 145 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.333A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.748A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.629A pdb=" N LYS D 105 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.113A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.580A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.808A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.592A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR H 119 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 removed outlier: 3.526A pdb=" N THR K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS K 111 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 Processing helix chain 'K' and resid 132 through 142 removed outlier: 3.639A pdb=" N LEU K 137 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL K 139 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU K 141 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 212 removed outlier: 3.733A pdb=" N GLN K 202 " --> pdb=" O PRO K 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU K 207 " --> pdb=" O GLY K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 240 Processing helix chain 'K' and resid 254 through 267 removed outlier: 3.507A pdb=" N LEU K 257 " --> pdb=" O LYS K 254 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN K 258 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP K 260 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG K 262 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE K 264 " --> pdb=" O LEU K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 289 removed outlier: 3.887A pdb=" N LEU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 328 through 330 No H-bonds generated for 'chain 'K' and resid 328 through 330' Processing helix chain 'K' and resid 335 through 340 Processing helix chain 'K' and resid 360 through 368 removed outlier: 3.578A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA K 365 " --> pdb=" O HIS K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 389 removed outlier: 3.527A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU K 388 " --> pdb=" O TRP K 384 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 406 Processing helix chain 'K' and resid 435 through 445 removed outlier: 4.126A pdb=" N LYS K 439 " --> pdb=" O SER K 435 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 444 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU K 445 " --> pdb=" O TYR K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 477 removed outlier: 3.649A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS K 475 " --> pdb=" O GLN K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 481 No H-bonds generated for 'chain 'K' and resid 479 through 481' Processing helix chain 'K' and resid 496 through 500 Processing helix chain 'K' and resid 503 through 517 removed outlier: 3.921A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 540 removed outlier: 3.778A pdb=" N ASP K 532 " --> pdb=" O SER K 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 555 through 564 Processing helix chain 'K' and resid 602 through 611 removed outlier: 3.703A pdb=" N ASP K 610 " --> pdb=" O LEU K 606 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 656 removed outlier: 3.781A pdb=" N LEU K 646 " --> pdb=" O GLN K 642 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN K 654 " --> pdb=" O VAL K 650 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG K 655 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR K 656 " --> pdb=" O GLN K 652 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 217 through 219 removed outlier: 3.504A pdb=" N LEU K 350 " --> pdb=" O GLY K 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 298 through 301 removed outlier: 6.896A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR K 320 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE K 251 " --> pdb=" O TYR K 320 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE K 322 " --> pdb=" O ILE K 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'K' and resid 425 through 431 removed outlier: 3.550A pdb=" N VAL K 593 " --> pdb=" O LYS K 622 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3268 1.33 - 1.45: 5062 1.45 - 1.57: 8060 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 17021 Sorted by residual: bond pdb=" BE BEF K1202 " pdb=" F2 BEF K1202 " ideal model delta sigma weight residual 1.476 1.709 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" BE BEF K1202 " pdb=" F1 BEF K1202 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 1.476 1.688 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.49e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 17016 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.68: 1639 105.68 - 113.37: 9683 113.37 - 121.07: 8492 121.07 - 128.77: 4233 128.77 - 136.47: 207 Bond angle restraints: 24254 Sorted by residual: angle pdb=" F1 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 120.12 98.86 21.26 3.00e+00 1.11e-01 5.02e+01 angle pdb=" F2 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 119.96 105.49 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N ILE K 329 " pdb=" CA ILE K 329 " pdb=" C ILE K 329 " ideal model delta sigma weight residual 111.91 108.14 3.77 8.90e-01 1.26e+00 1.79e+01 angle pdb=" C SER D 75 " pdb=" N ARG D 76 " pdb=" CA ARG D 76 " ideal model delta sigma weight residual 121.58 114.57 7.01 1.95e+00 2.63e-01 1.29e+01 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.58 114.72 6.86 1.95e+00 2.63e-01 1.24e+01 ... (remaining 24249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 7671 30.90 - 61.80: 1541 61.80 - 92.70: 35 92.70 - 123.60: 0 123.60 - 154.50: 6 Dihedral angle restraints: 9253 sinusoidal: 5561 harmonic: 3692 Sorted by residual: dihedral pdb=" O2A ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PA ADP K1201 " pdb=" PB ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 84.35 -144.34 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PB ADP K1201 " pdb=" PA ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.54 -142.54 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP K1201 " pdb=" O5' ADP K1201 " pdb=" PA ADP K1201 " pdb=" O2A ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 82.45 -142.44 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 9250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2206 0.059 - 0.119: 491 0.119 - 0.178: 52 0.178 - 0.238: 5 0.238 - 0.297: 1 Chirality restraints: 2755 Sorted by residual: chirality pdb=" CA THR K 492 " pdb=" N THR K 492 " pdb=" C THR K 492 " pdb=" CB THR K 492 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2752 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO K 489 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 406 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO K 407 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO K 407 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 407 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO K 490 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.036 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 304 2.65 - 3.21: 12839 3.21 - 3.77: 28128 3.77 - 4.34: 37285 4.34 - 4.90: 54234 Nonbonded interactions: 132790 Sorted by model distance: nonbonded pdb=" O3B ADP K1201 " pdb="MG MG K1203 " model vdw 2.086 2.170 nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.254 2.496 nonbonded pdb=" N2 DG I 83 " pdb=" O2 DC J 65 " model vdw 2.310 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.334 2.440 nonbonded pdb=" O THR K 492 " pdb=" OG1 THR K 493 " model vdw 2.354 2.440 ... (remaining 132785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 46.290 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.008 0.233 17021 Z= 0.479 Angle : 0.848 21.257 24254 Z= 0.487 Chirality : 0.048 0.297 2755 Planarity : 0.007 0.094 2063 Dihedral : 24.451 154.504 6861 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.00 % Rotamer Outliers : 0.28 % 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: -3.67 (0.19), residues: 1241 helix: -1.94 (0.14), residues: 740 sheet: -3.11 (0.63), residues: 61 loop : -2.98 (0.24), residues: 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 228 average time/residue: 0.4251 time to fit residues: 128.1497 Evaluate side-chains 151 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5055 time to fit residues: 3.8389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS D 81 ASN E 68 GLN E 108 ASN F 93 GLN G 110 ASN H 81 ASN K 205 ASN K 437 GLN K 500 ASN K 526 GLN ** K 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17021 Z= 0.201 Angle : 0.611 6.830 24254 Z= 0.353 Chirality : 0.037 0.173 2755 Planarity : 0.005 0.062 2063 Dihedral : 29.534 155.380 4338 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1241 helix: -0.19 (0.18), residues: 763 sheet: -2.68 (0.65), residues: 59 loop : -2.64 (0.26), residues: 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 167 average time/residue: 0.3207 time to fit residues: 76.7698 Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1502 time to fit residues: 3.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 0.2980 chunk 147 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 81 ASN F 93 GLN K 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17021 Z= 0.216 Angle : 0.550 6.110 24254 Z= 0.321 Chirality : 0.035 0.155 2755 Planarity : 0.004 0.056 2063 Dihedral : 29.079 178.754 4338 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1241 helix: 0.63 (0.19), residues: 769 sheet: -2.34 (0.68), residues: 57 loop : -2.42 (0.27), residues: 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 160 average time/residue: 0.3226 time to fit residues: 73.6836 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1469 time to fit residues: 2.8602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 overall best weight: 1.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17021 Z= 0.200 Angle : 0.531 6.143 24254 Z= 0.311 Chirality : 0.035 0.151 2755 Planarity : 0.004 0.047 2063 Dihedral : 28.881 171.826 4338 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1241 helix: 1.25 (0.20), residues: 763 sheet: -1.96 (0.69), residues: 57 loop : -2.23 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.586 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 152 average time/residue: 0.3443 time to fit residues: 76.1570 Evaluate side-chains 139 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1612 time to fit residues: 2.4290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.047 17021 Z= 0.510 Angle : 0.678 6.623 24254 Z= 0.384 Chirality : 0.042 0.150 2755 Planarity : 0.005 0.048 2063 Dihedral : 29.176 149.967 4338 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 1.11 % 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: -0.16 (0.25), residues: 1241 helix: 1.17 (0.19), residues: 763 sheet: -2.13 (0.74), residues: 52 loop : -2.26 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.416 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 138 average time/residue: 0.3248 time to fit residues: 65.1124 Evaluate side-chains 127 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1696 time to fit residues: 3.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 93 GLN ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17021 Z= 0.158 Angle : 0.540 8.516 24254 Z= 0.314 Chirality : 0.034 0.161 2755 Planarity : 0.004 0.046 2063 Dihedral : 28.666 150.257 4338 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1241 helix: 1.61 (0.20), residues: 758 sheet: -1.90 (0.62), residues: 67 loop : -1.98 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.431 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 158 average time/residue: 0.3172 time to fit residues: 72.5946 Evaluate side-chains 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1457 time to fit residues: 2.6634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 81 ASN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 17021 Z= 0.297 Angle : 0.580 7.577 24254 Z= 0.332 Chirality : 0.036 0.150 2755 Planarity : 0.004 0.045 2063 Dihedral : 28.690 149.636 4338 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1241 helix: 1.72 (0.20), residues: 755 sheet: -1.75 (0.67), residues: 62 loop : -1.92 (0.30), residues: 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.456 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 139 average time/residue: 0.3119 time to fit residues: 63.0446 Evaluate side-chains 135 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1484 time to fit residues: 2.1928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 0.0040 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 17021 Z= 0.226 Angle : 0.564 7.947 24254 Z= 0.323 Chirality : 0.035 0.155 2755 Planarity : 0.004 0.043 2063 Dihedral : 28.601 149.464 4338 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1241 helix: 1.79 (0.20), residues: 755 sheet: -1.64 (0.64), residues: 67 loop : -1.87 (0.29), residues: 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.441 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.3170 time to fit residues: 65.4121 Evaluate side-chains 136 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 81 ASN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.036 17021 Z= 0.332 Angle : 0.601 7.537 24254 Z= 0.341 Chirality : 0.037 0.150 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.719 149.056 4338 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1241 helix: 1.77 (0.20), residues: 752 sheet: -1.52 (0.68), residues: 62 loop : -1.90 (0.29), residues: 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.599 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 132 average time/residue: 0.3446 time to fit residues: 65.5115 Evaluate side-chains 132 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1499 time to fit residues: 2.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 36 optimal weight: 0.0030 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 17021 Z= 0.305 Angle : 0.595 7.890 24254 Z= 0.339 Chirality : 0.037 0.151 2755 Planarity : 0.004 0.042 2063 Dihedral : 28.697 149.131 4338 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1241 helix: 1.74 (0.20), residues: 758 sheet: -1.45 (0.68), residues: 62 loop : -1.88 (0.29), residues: 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.517 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.3538 time to fit residues: 67.2890 Evaluate side-chains 130 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN K 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.069991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.046096 restraints weight = 63645.370| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.68 r_work: 0.2665 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17021 Z= 0.165 Angle : 0.549 8.405 24254 Z= 0.315 Chirality : 0.034 0.154 2755 Planarity : 0.004 0.041 2063 Dihedral : 28.408 149.037 4338 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1241 helix: 1.84 (0.20), residues: 763 sheet: -1.26 (0.65), residues: 67 loop : -1.73 (0.30), residues: 411 =============================================================================== Job complete usr+sys time: 2841.77 seconds wall clock time: 52 minutes 23.85 seconds (3143.85 seconds total)