Starting phenix.real_space_refine on Fri Dec 8 02:15:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn0_30412/12_2023/7cn0_30412.pdb" } resolution = 3.9 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 24 5.16 5 C 4412 2.51 5 N 1076 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 541": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "D ARG 541": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6602 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.15, per 1000 atoms: 0.63 Number of scatterers: 6602 At special positions: 0 Unit cell: (106.964, 106.964, 77.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 24 16.00 O 1088 8.00 N 1076 7.00 C 4412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 538' Processing helix chain 'A' and resid 548 through 575 Processing helix chain 'A' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 548 through 575 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 538' Processing helix chain 'C' and resid 548 through 575 Processing helix chain 'C' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 456 through 473 removed outlier: 3.874A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 497 removed outlier: 4.407A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.796A pdb=" N ARG D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 538' Processing helix chain 'D' and resid 548 through 575 Processing helix chain 'D' and resid 585 through 593 removed outlier: 3.795A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 624 removed outlier: 4.002A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 666 removed outlier: 4.058A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1964 1.34 - 1.46: 1484 1.46 - 1.57: 3272 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6756 Sorted by residual: bond pdb=" C THR D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR C 425 " pdb=" N PRO C 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" C THR A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" CA ILE A 521 " pdb=" CB ILE A 521 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.77e-01 ... (remaining 6751 not shown) Histogram of bond angle deviations from ideal: 101.11 - 107.69: 252 107.69 - 114.28: 4016 114.28 - 120.86: 3108 120.86 - 127.44: 1764 127.44 - 134.03: 84 Bond angle restraints: 9224 Sorted by residual: angle pdb=" N PHE A 498 " pdb=" CA PHE A 498 " pdb=" C PHE A 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE B 498 " pdb=" CA PHE B 498 " pdb=" C PHE B 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE C 498 " pdb=" CA PHE C 498 " pdb=" C PHE C 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" N PHE D 498 " pdb=" CA PHE D 498 " pdb=" C PHE D 498 " ideal model delta sigma weight residual 114.62 111.11 3.51 1.14e+00 7.69e-01 9.47e+00 angle pdb=" CA PHE C 498 " pdb=" C PHE C 498 " pdb=" N LEU C 499 " ideal model delta sigma weight residual 119.71 116.85 2.86 1.17e+00 7.31e-01 5.97e+00 ... (remaining 9219 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.01: 3108 10.01 - 20.02: 452 20.02 - 30.02: 184 30.02 - 40.03: 68 40.03 - 50.03: 32 Dihedral angle restraints: 3844 sinusoidal: 1292 harmonic: 2552 Sorted by residual: dihedral pdb=" CA PHE C 656 " pdb=" C PHE C 656 " pdb=" N GLY C 657 " pdb=" CA GLY C 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE D 656 " pdb=" C PHE D 656 " pdb=" N GLY D 657 " pdb=" CA GLY D 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE A 656 " pdb=" C PHE A 656 " pdb=" N GLY A 657 " pdb=" CA GLY A 657 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 744 0.036 - 0.071: 312 0.071 - 0.107: 56 0.107 - 0.142: 20 0.142 - 0.178: 4 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA THR C 425 " pdb=" N THR C 425 " pdb=" C THR C 425 " pdb=" CB THR C 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA THR D 425 " pdb=" N THR D 425 " pdb=" C THR D 425 " pdb=" CB THR D 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA THR B 425 " pdb=" N THR B 425 " pdb=" C THR B 425 " pdb=" CB THR B 425 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 1133 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 616 " 0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR C 616 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 616 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 616 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 616 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 616 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 616 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 616 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 616 " -0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR B 616 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 616 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 616 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 616 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 616 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 616 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 616 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 616 " -0.010 2.00e-02 2.50e+03 7.61e-03 1.16e+00 pdb=" CG TYR A 616 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 616 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 616 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 616 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 616 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 616 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 616 " -0.002 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 32 2.50 - 3.16: 5920 3.16 - 3.82: 12816 3.82 - 4.48: 15316 4.48 - 5.14: 25262 Nonbonded interactions: 59346 Sorted by model distance: nonbonded pdb=" CG LEU A 646 " pdb=" CE MET D 554 " model vdw 1.843 3.890 nonbonded pdb=" CE MET A 554 " pdb=" CG LEU B 646 " model vdw 1.843 3.890 nonbonded pdb=" CE MET B 554 " pdb=" CG LEU C 646 " model vdw 1.843 3.890 nonbonded pdb=" CE MET C 554 " pdb=" CG LEU D 646 " model vdw 1.844 3.890 nonbonded pdb=" CD2 LEU A 646 " pdb=" CE MET D 554 " model vdw 1.867 3.880 ... (remaining 59341 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 402 through 666) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.000 Extract box with map and model: 9.870 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.110 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.004 0.023 6756 Z= 0.227 Angle : 0.623 5.810 9224 Z= 0.347 Chirality : 0.041 0.178 1136 Planarity : 0.003 0.016 1100 Dihedral : 13.322 50.033 2188 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.25), residues: 836 helix: -1.49 (0.17), residues: 644 sheet: None (None), residues: 0 loop : -2.85 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 585 HIS 0.002 0.001 HIS A 492 PHE 0.011 0.001 PHE B 640 TYR 0.018 0.002 TYR C 616 ARG 0.001 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.742 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1859 time to fit residues: 39.2901 Evaluate side-chains 121 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 562 HIS A 576 GLN A 587 HIS A 588 ASN B 470 ASN B 562 HIS B 576 GLN B 587 HIS B 588 ASN C 470 ASN C 562 HIS C 576 GLN C 587 HIS C 588 ASN D 470 ASN D 562 HIS D 576 GLN D 587 HIS D 588 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6756 Z= 0.191 Angle : 0.574 6.365 9224 Z= 0.289 Chirality : 0.040 0.156 1136 Planarity : 0.003 0.023 1100 Dihedral : 4.663 17.402 920 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.47 % Allowed : 22.84 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.28), residues: 836 helix: -0.41 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -2.23 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 585 HIS 0.001 0.000 HIS A 492 PHE 0.014 0.001 PHE A 617 TYR 0.014 0.002 TYR B 420 ARG 0.004 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 0.755 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 160 average time/residue: 0.1582 time to fit residues: 34.2961 Evaluate side-chains 144 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0593 time to fit residues: 2.2020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6756 Z= 0.172 Angle : 0.565 6.320 9224 Z= 0.285 Chirality : 0.040 0.156 1136 Planarity : 0.003 0.025 1100 Dihedral : 4.438 16.421 920 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.23 % Allowed : 29.01 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.29), residues: 836 helix: -0.02 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.99 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 585 HIS 0.001 0.000 HIS B 562 PHE 0.010 0.001 PHE A 640 TYR 0.011 0.001 TYR A 616 ARG 0.006 0.001 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.732 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 167 average time/residue: 0.1648 time to fit residues: 37.1148 Evaluate side-chains 143 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6756 Z= 0.175 Angle : 0.567 6.279 9224 Z= 0.283 Chirality : 0.040 0.158 1136 Planarity : 0.004 0.034 1100 Dihedral : 4.342 16.775 920 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.55 % Allowed : 31.79 % Favored : 64.66 % 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: -0.47 (0.30), residues: 836 helix: 0.17 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.73 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 585 HIS 0.001 0.000 HIS A 492 PHE 0.010 0.001 PHE A 640 TYR 0.009 0.001 TYR C 616 ARG 0.008 0.001 ARG C 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.741 Fit side-chains outliers start: 23 outliers final: 0 residues processed: 164 average time/residue: 0.1742 time to fit residues: 38.3923 Evaluate side-chains 140 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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: 0.7687 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.213 Angle : 0.595 6.276 9224 Z= 0.299 Chirality : 0.042 0.161 1136 Planarity : 0.003 0.023 1100 Dihedral : 4.387 17.230 920 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.70 % Allowed : 31.94 % Favored : 64.35 % 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: -0.41 (0.29), residues: 836 helix: 0.20 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.64 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 585 HIS 0.001 0.001 HIS D 485 PHE 0.012 0.001 PHE A 640 TYR 0.012 0.002 TYR D 542 ARG 0.002 0.000 ARG C 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.701 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 153 average time/residue: 0.1547 time to fit residues: 32.8700 Evaluate side-chains 157 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0659 time to fit residues: 3.2722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7670 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6756 Z= 0.173 Angle : 0.566 6.296 9224 Z= 0.280 Chirality : 0.041 0.147 1136 Planarity : 0.003 0.024 1100 Dihedral : 4.309 17.661 920 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.23 % Allowed : 34.10 % Favored : 64.66 % 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: -0.18 (0.30), residues: 836 helix: 0.33 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.45 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 585 HIS 0.001 0.000 HIS D 485 PHE 0.020 0.002 PHE D 617 TYR 0.011 0.002 TYR D 652 ARG 0.001 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.687 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.1751 time to fit residues: 36.4933 Evaluate side-chains 140 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 588 ASN C 588 ASN D 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.002 0.022 6756 Z= 0.158 Angle : 0.579 7.244 9224 Z= 0.278 Chirality : 0.040 0.143 1136 Planarity : 0.003 0.033 1100 Dihedral : 4.280 17.576 920 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.85 % Allowed : 35.19 % Favored : 62.96 % 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: -0.03 (0.30), residues: 836 helix: 0.42 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.34 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 585 HIS 0.001 0.000 HIS D 587 PHE 0.018 0.001 PHE D 617 TYR 0.009 0.001 TYR B 652 ARG 0.001 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.782 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 152 average time/residue: 0.1477 time to fit residues: 31.5115 Evaluate side-chains 148 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0689 time to fit residues: 2.5414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6756 Z= 0.213 Angle : 0.604 6.266 9224 Z= 0.297 Chirality : 0.042 0.166 1136 Planarity : 0.004 0.036 1100 Dihedral : 4.446 18.147 920 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 35.96 % Favored : 64.04 % 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: -0.04 (0.30), residues: 836 helix: 0.42 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.26 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 585 HIS 0.001 0.001 HIS A 492 PHE 0.016 0.002 PHE D 617 TYR 0.011 0.002 TYR A 616 ARG 0.002 0.000 ARG D 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.753 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1513 time to fit residues: 31.6525 Evaluate side-chains 144 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6756 Z= 0.176 Angle : 0.585 6.241 9224 Z= 0.288 Chirality : 0.041 0.160 1136 Planarity : 0.003 0.026 1100 Dihedral : 4.337 18.323 920 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 36.42 % Favored : 63.58 % 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: 0.08 (0.30), residues: 836 helix: 0.50 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.23 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 585 HIS 0.001 0.000 HIS C 587 PHE 0.025 0.002 PHE A 617 TYR 0.009 0.001 TYR C 616 ARG 0.001 0.000 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.739 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1488 time to fit residues: 30.4017 Evaluate side-chains 142 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6756 Z= 0.159 Angle : 0.594 6.203 9224 Z= 0.286 Chirality : 0.041 0.154 1136 Planarity : 0.003 0.027 1100 Dihedral : 4.255 17.849 920 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 37.96 % Favored : 62.04 % 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: 0.11 (0.30), residues: 836 helix: 0.50 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.21 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 585 HIS 0.001 0.000 HIS B 492 PHE 0.024 0.002 PHE A 617 TYR 0.007 0.001 TYR D 616 ARG 0.001 0.000 ARG D 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.805 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1563 time to fit residues: 30.3850 Evaluate side-chains 135 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.170872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128014 restraints weight = 11918.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130645 restraints weight = 7139.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132246 restraints weight = 5202.571| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6756 Z= 0.175 Angle : 0.599 6.153 9224 Z= 0.293 Chirality : 0.042 0.160 1136 Planarity : 0.003 0.029 1100 Dihedral : 4.354 19.502 920 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 37.96 % Favored : 62.04 % 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: 0.18 (0.30), residues: 836 helix: 0.56 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.27 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 585 HIS 0.001 0.000 HIS B 492 PHE 0.024 0.002 PHE A 617 TYR 0.008 0.001 TYR D 616 ARG 0.002 0.000 ARG D 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1483.85 seconds wall clock time: 27 minutes 47.45 seconds (1667.45 seconds total)