Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 16:29:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/08_2023/7lys_23600.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.171 sd= 1.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 282": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 595": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 697": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 5.85, per 1000 atoms: 0.43 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 10.78 Conformation dependent library (CDL) restraints added in 998.5 milliseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" O4' DC C 3 " pdb=" C1' DC C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.65e-01 bond pdb=" O4' DT D -5 " pdb=" C1' DT D -5 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.57e-01 bond pdb=" CB ARG A 488 " pdb=" CG ARG A 488 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 769 106.98 - 113.72: 15785 113.72 - 120.47: 5006 120.47 - 127.22: 3356 127.22 - 133.97: 231 Bond angle restraints: 25147 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 angle pdb=" C3' DC D 5 " pdb=" C2' DC D 5 " pdb=" C1' DC D 5 " ideal model delta sigma weight residual 101.60 104.72 -3.12 1.50e+00 4.44e-01 4.33e+00 angle pdb=" C4' DC D -9 " pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 110.00 113.04 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 102.40 105.03 -2.63 1.50e+00 4.44e-01 3.08e+00 angle pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " pdb=" C1' DT C -8 " ideal model delta sigma weight residual 101.60 104.10 -2.50 1.50e+00 4.44e-01 2.79e+00 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5177 33.78 - 67.57: 253 67.57 - 101.35: 9 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 5441 sinusoidal: 3183 harmonic: 2258 Sorted by residual: dihedral pdb=" CA PRO A 171 " pdb=" C PRO A 171 " pdb=" N GLU A 172 " pdb=" CA GLU A 172 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 236 " pdb=" C VAL A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE A 653 " pdb=" C PHE A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 779 0.029 - 0.058: 297 0.058 - 0.087: 62 0.087 - 0.117: 61 0.117 - 0.146: 8 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 1.850 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 1.850 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 1.850 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 1.850 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 1.850 ... (remaining 181320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.200 Extract box with map and model: 3.090 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.590 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7535 Z= 0.210 Angle : 0.540 4.141 10601 Z= 0.315 Chirality : 0.038 0.146 1207 Planarity : 0.003 0.032 1048 Dihedral : 17.650 168.916 3042 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.17 % 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: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.5172 time to fit residues: 60.5900 Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7535 Z= 0.199 Angle : 0.553 3.926 10601 Z= 0.312 Chirality : 0.039 0.152 1207 Planarity : 0.004 0.036 1048 Dihedral : 18.069 168.781 1706 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.35 % 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: -0.34 (0.32), residues: 663 helix: 0.88 (0.30), residues: 302 sheet: -1.32 (0.58), residues: 74 loop : -1.07 (0.36), residues: 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.5720 time to fit residues: 56.6766 Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1507 time to fit residues: 1.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 18 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7535 Z= 0.203 Angle : 0.528 4.706 10601 Z= 0.296 Chirality : 0.038 0.138 1207 Planarity : 0.004 0.036 1048 Dihedral : 18.047 170.762 1706 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.35 % 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 (0.33), residues: 663 helix: 1.49 (0.31), residues: 304 sheet: -1.74 (0.55), residues: 79 loop : -0.83 (0.37), residues: 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.5912 time to fit residues: 55.0662 Evaluate side-chains 69 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1480 time to fit residues: 1.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7535 Z= 0.173 Angle : 0.514 4.976 10601 Z= 0.288 Chirality : 0.037 0.138 1207 Planarity : 0.004 0.036 1048 Dihedral : 17.985 170.202 1706 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.70 % 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: 0.56 (0.34), residues: 663 helix: 1.73 (0.31), residues: 305 sheet: -1.47 (0.57), residues: 72 loop : -0.57 (0.38), residues: 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.5869 time to fit residues: 55.5584 Evaluate side-chains 69 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1588 time to fit residues: 1.6911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7535 Z= 0.223 Angle : 0.528 5.162 10601 Z= 0.294 Chirality : 0.039 0.135 1207 Planarity : 0.004 0.034 1048 Dihedral : 17.975 169.843 1706 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.35 % 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: 0.56 (0.34), residues: 663 helix: 1.77 (0.31), residues: 306 sheet: -1.65 (0.56), residues: 72 loop : -0.57 (0.38), residues: 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.6433 time to fit residues: 57.3170 Evaluate side-chains 69 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1496 time to fit residues: 1.6736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.168 Angle : 0.506 4.024 10601 Z= 0.283 Chirality : 0.037 0.135 1207 Planarity : 0.004 0.053 1048 Dihedral : 17.949 169.883 1706 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.52 % 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: 0.75 (0.34), residues: 663 helix: 1.93 (0.31), residues: 306 sheet: -1.55 (0.57), residues: 72 loop : -0.49 (0.38), residues: 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.5860 time to fit residues: 52.1270 Evaluate side-chains 71 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1707 time to fit residues: 1.6904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.183 Angle : 0.508 4.218 10601 Z= 0.283 Chirality : 0.038 0.134 1207 Planarity : 0.004 0.045 1048 Dihedral : 17.920 169.635 1706 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.89 (0.34), residues: 663 helix: 1.98 (0.31), residues: 306 sheet: -1.13 (0.62), residues: 62 loop : -0.49 (0.37), residues: 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.003 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.6042 time to fit residues: 51.1797 Evaluate side-chains 69 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 7535 Z= 0.148 Angle : 0.496 5.011 10601 Z= 0.277 Chirality : 0.037 0.137 1207 Planarity : 0.004 0.040 1048 Dihedral : 17.895 169.616 1706 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.17 % 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: 1.00 (0.34), residues: 663 helix: 2.08 (0.31), residues: 305 sheet: -1.02 (0.61), residues: 64 loop : -0.44 (0.38), residues: 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.933 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.5853 time to fit residues: 56.0170 Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1562 time to fit residues: 1.4193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.165 Angle : 0.501 3.935 10601 Z= 0.279 Chirality : 0.037 0.132 1207 Planarity : 0.004 0.038 1048 Dihedral : 17.871 169.286 1706 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 1.02 (0.34), residues: 663 helix: 2.12 (0.31), residues: 305 sheet: -0.97 (0.60), residues: 64 loop : -0.46 (0.38), residues: 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.992 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.5974 time to fit residues: 53.6621 Evaluate side-chains 70 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.171 Angle : 0.502 4.250 10601 Z= 0.280 Chirality : 0.037 0.131 1207 Planarity : 0.004 0.061 1048 Dihedral : 17.870 169.074 1706 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 1.06 (0.34), residues: 663 helix: 2.11 (0.31), residues: 305 sheet: -0.84 (0.60), residues: 62 loop : -0.42 (0.38), residues: 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.841 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.6324 time to fit residues: 57.3444 Evaluate side-chains 70 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069135 restraints weight = 42669.803| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.64 r_work: 0.2894 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.166 Angle : 0.499 4.207 10601 Z= 0.279 Chirality : 0.037 0.131 1207 Planarity : 0.004 0.052 1048 Dihedral : 17.845 168.940 1706 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 1.11 (0.34), residues: 663 helix: 2.14 (0.31), residues: 305 sheet: -0.77 (0.60), residues: 62 loop : -0.40 (0.38), residues: 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.65 seconds wall clock time: 67 minutes 18.90 seconds (4038.90 seconds total)