Starting phenix.real_space_refine (version: dev) on Tue Dec 13 15:49:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/12_2022/6jyl_9718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/12_2022/6jyl_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_9718/12_2022/6jyl_9718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/12_2022/6jyl_9718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/12_2022/6jyl_9718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jyl_9718/12_2022/6jyl_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 Convert atoms to be neutral 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 9.91, per 1000 atoms: 0.61 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: 8.34 Conformation dependent library (CDL) restraints added in 1.7 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: 6.90 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: 7.86 Time building geometry restraints manager: 8.86 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 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. 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.660 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 53.370 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 2.78 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 : 1.350 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: 0.4033 time to fit residues: 122.7688 Evaluate side-chains 151 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4791 time to fit residues: 3.6481 ------------------------------------------------------------------------------- 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: 0.8667 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 : 6.50 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 : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 167 average time/residue: 0.3126 time to fit residues: 75.2452 Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1461 time to fit residues: 3.7106 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.8671 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 : 29.079 178.757 4338 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.57 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 : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 160 average time/residue: 0.2976 time to fit residues: 68.3505 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1400 time to fit residues: 2.7016 ------------------------------------------------------------------------------- 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: 8.9990 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17021 Z= 0.233 Angle : 0.544 6.110 24254 Z= 0.317 Chirality : 0.035 0.150 2755 Planarity : 0.004 0.048 2063 Dihedral : 28.916 169.578 4338 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -0.10 (0.25), residues: 1241 helix: 1.23 (0.20), residues: 761 sheet: -1.99 (0.70), residues: 57 loop : -2.24 (0.28), residues: 423 *********************** 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 155 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.482 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 150 average time/residue: 0.3019 time to fit residues: 65.6753 Evaluate side-chains 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1569 time to fit residues: 2.4705 ------------------------------------------------------------------------------- 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: 8.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 0.0000 chunk 36 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS G 112 GLN H 81 ASN ** 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: 0.8700 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 17021 Z= 0.299 Angle : 0.574 6.448 24254 Z= 0.331 Chirality : 0.037 0.156 2755 Planarity : 0.004 0.048 2063 Dihedral : 28.824 150.068 4338 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % 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: 0.20 (0.25), residues: 1241 helix: 1.45 (0.20), residues: 760 sheet: -1.86 (0.75), residues: 52 loop : -2.10 (0.29), residues: 429 *********************** 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 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.639 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 149 average time/residue: 0.3062 time to fit residues: 66.7072 Evaluate side-chains 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1387 time to fit residues: 2.8670 ------------------------------------------------------------------------------- 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: 4.9990 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 17021 Z= 0.274 Angle : 0.565 7.550 24254 Z= 0.326 Chirality : 0.036 0.154 2755 Planarity : 0.004 0.047 2063 Dihedral : 28.721 149.934 4338 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.25), residues: 1241 helix: 1.58 (0.20), residues: 760 sheet: -1.83 (0.63), residues: 67 loop : -1.99 (0.30), residues: 414 *********************** 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 151 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.767 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 145 average time/residue: 0.2993 time to fit residues: 63.3086 Evaluate side-chains 138 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1443 time to fit residues: 2.6551 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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: 0.8700 moved from start: 0.2723 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= 0.300 Angle : 0.578 7.626 24254 Z= 0.332 Chirality : 0.037 0.150 2755 Planarity : 0.004 0.046 2063 Dihedral : 28.701 149.827 4338 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.46 % 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: 0.48 (0.25), residues: 1241 helix: 1.69 (0.20), residues: 756 sheet: -1.73 (0.67), residues: 62 loop : -1.97 (0.29), residues: 423 *********************** 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 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.610 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.3062 time to fit residues: 62.3698 Evaluate side-chains 132 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1290 time to fit residues: 2.0538 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN K 601 ASN K 613 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17021 Z= 0.163 Angle : 0.531 8.499 24254 Z= 0.307 Chirality : 0.034 0.153 2755 Planarity : 0.004 0.045 2063 Dihedral : 28.396 149.360 4338 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: 0.78 (0.25), residues: 1241 helix: 1.84 (0.20), residues: 758 sheet: -1.49 (0.64), residues: 67 loop : -1.69 (0.30), residues: 416 *********************** 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 155 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.534 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 153 average time/residue: 0.2959 time to fit residues: 66.9355 Evaluate side-chains 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1389 time to fit residues: 2.3567 ------------------------------------------------------------------------------- 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: 10.0000 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 17021 Z= 0.228 Angle : 0.558 8.182 24254 Z= 0.319 Chirality : 0.035 0.148 2755 Planarity : 0.004 0.043 2063 Dihedral : 28.479 148.881 4338 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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: 0.82 (0.25), residues: 1241 helix: 1.92 (0.20), residues: 755 sheet: -1.36 (0.64), residues: 67 loop : -1.78 (0.30), residues: 419 *********************** 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 142 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.758 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.3146 time to fit residues: 65.7775 Evaluate side-chains 137 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1789 time to fit residues: 2.1179 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 213 ASN ** 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: 0.8695 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 17021 Z= 0.297 Angle : 0.588 7.678 24254 Z= 0.334 Chirality : 0.036 0.146 2755 Planarity : 0.004 0.041 2063 Dihedral : 28.591 148.787 4338 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.00 % 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: 0.78 (0.25), residues: 1241 helix: 1.88 (0.20), residues: 752 sheet: -1.33 (0.64), residues: 67 loop : -1.78 (0.29), residues: 422 ********************** 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 134 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.625 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3088 time to fit residues: 60.0539 Evaluate side-chains 130 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6391 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.044979 restraints weight = 63605.292| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.71 r_work: 0.2621 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 17021 Z= 0.201 Angle : 0.556 8.250 24254 Z= 0.319 Chirality : 0.034 0.151 2755 Planarity : 0.004 0.041 2063 Dihedral : 28.473 148.725 4338 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: 0.83 (0.25), residues: 1241 helix: 1.90 (0.20), residues: 758 sheet: -1.14 (0.65), residues: 67 loop : -1.79 (0.29), residues: 416 =============================================================================== Job complete usr+sys time: 2636.23 seconds wall clock time: 48 minutes 41.77 seconds (2921.77 seconds total)