Starting phenix.real_space_refine on Tue Feb 13 13:32:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcn_13897/02_2024/7qcn_13897.pdb" } resolution = 3.4 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= -0.001 sd= 0.009 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 Ca 2 9.91 5 S 90 5.16 5 C 4012 2.51 5 N 1030 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 4474": "OD1" <-> "OD2" Residue "B ASP 4474": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6416 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3104 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3104 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.26, per 1000 atoms: 0.51 Number of scatterers: 6416 At special positions: 0 Unit cell: (93.74, 112.66, 104.06, 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) Ca 2 19.99 S 90 16.00 O 1282 8.00 N 1030 7.00 C 4012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A4363 " - pdb=" SG CYS A4386 " distance=2.03 Simple disulfide: pdb=" SG CYS A4379 " - pdb=" SG CYS B4379 " distance=2.09 Simple disulfide: pdb=" SG CYS A4381 " - pdb=" SG CYS A4422 " distance=2.03 Simple disulfide: pdb=" SG CYS A4399 " - pdb=" SG CYS A4423 " distance=2.03 Simple disulfide: pdb=" SG CYS A4407 " - pdb=" SG CYS A4428 " distance=2.05 Simple disulfide: pdb=" SG CYS A4430 " - pdb=" SG CYS A4576 " distance=2.03 Simple disulfide: pdb=" SG CYS A4432 " - pdb=" SG CYS A4573 " distance=2.03 Simple disulfide: pdb=" SG CYS A4454 " - pdb=" SG CYS A4612 " distance=2.02 Simple disulfide: pdb=" SG CYS A4478 " - pdb=" SG CYS A4486 " distance=2.04 Simple disulfide: pdb=" SG CYS A4584 " - pdb=" SG CYS A4595 " distance=2.02 Simple disulfide: pdb=" SG CYS A4638 " - pdb=" SG CYS A4673 " distance=2.03 Simple disulfide: pdb=" SG CYS A4644 " - pdb=" SG CYS A4668 " distance=2.03 Simple disulfide: pdb=" SG CYS A4655 " - pdb=" SG CYS A4692 " distance=1.99 Simple disulfide: pdb=" SG CYS A4682 " - pdb=" SG CYS A4709 " distance=2.04 Simple disulfide: pdb=" SG CYS A4698 " - pdb=" SG CYS A4722 " distance=2.03 Simple disulfide: pdb=" SG CYS A4713 " - pdb=" SG CYS A4746 " distance=2.03 Simple disulfide: pdb=" SG CYS A4730 " - pdb=" SG CYS A4766 " distance=2.02 Simple disulfide: pdb=" SG CYS A4748 " - pdb=" SG CYS A4762 " distance=2.03 Simple disulfide: pdb=" SG CYS A4768 " - pdb=" SG CYS A4791 " distance=2.04 Simple disulfide: pdb=" SG CYS A4789 " - pdb=" SG CYS A4800 " distance=2.04 Simple disulfide: pdb=" SG CYS B4363 " - pdb=" SG CYS B4386 " distance=2.03 Simple disulfide: pdb=" SG CYS B4381 " - pdb=" SG CYS B4422 " distance=2.03 Simple disulfide: pdb=" SG CYS B4399 " - pdb=" SG CYS B4423 " distance=2.03 Simple disulfide: pdb=" SG CYS B4407 " - pdb=" SG CYS B4428 " distance=2.05 Simple disulfide: pdb=" SG CYS B4430 " - pdb=" SG CYS B4576 " distance=2.03 Simple disulfide: pdb=" SG CYS B4432 " - pdb=" SG CYS B4573 " distance=2.03 Simple disulfide: pdb=" SG CYS B4454 " - pdb=" SG CYS B4612 " distance=2.02 Simple disulfide: pdb=" SG CYS B4478 " - pdb=" SG CYS B4486 " distance=2.04 Simple disulfide: pdb=" SG CYS B4584 " - pdb=" SG CYS B4595 " distance=2.02 Simple disulfide: pdb=" SG CYS B4638 " - pdb=" SG CYS B4673 " distance=2.03 Simple disulfide: pdb=" SG CYS B4644 " - pdb=" SG CYS B4668 " distance=2.03 Simple disulfide: pdb=" SG CYS B4655 " - pdb=" SG CYS B4692 " distance=1.99 Simple disulfide: pdb=" SG CYS B4682 " - pdb=" SG CYS B4709 " distance=2.04 Simple disulfide: pdb=" SG CYS B4698 " - pdb=" SG CYS B4722 " distance=2.03 Simple disulfide: pdb=" SG CYS B4713 " - pdb=" SG CYS B4746 " distance=2.03 Simple disulfide: pdb=" SG CYS B4730 " - pdb=" SG CYS B4766 " distance=2.02 Simple disulfide: pdb=" SG CYS B4748 " - pdb=" SG CYS B4762 " distance=2.03 Simple disulfide: pdb=" SG CYS B4768 " - pdb=" SG CYS B4791 " distance=2.04 Simple disulfide: pdb=" SG CYS B4789 " - pdb=" SG CYS B4800 " distance=2.04 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A5203 " - " ASN A4703 " " NAG A5204 " - " ASN A4738 " " NAG B5203 " - " ASN B4703 " " NAG B5204 " - " ASN B4738 " " NAG C 1 " - " ASN A4578 " " NAG D 1 " - " ASN B4578 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 15.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 4594 through 4599 removed outlier: 3.663A pdb=" N ALA A4598 " --> pdb=" O ASN A4594 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A4599 " --> pdb=" O CYS A4595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4594 through 4599' Processing helix chain 'A' and resid 4600 through 4602 No H-bonds generated for 'chain 'A' and resid 4600 through 4602' Processing helix chain 'A' and resid 4641 through 4646 Processing helix chain 'A' and resid 4647 through 4649 No H-bonds generated for 'chain 'A' and resid 4647 through 4649' Processing helix chain 'A' and resid 4651 through 4655 removed outlier: 4.212A pdb=" N GLN A4654 " --> pdb=" O LEU A4651 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4675 removed outlier: 3.908A pdb=" N MET A4675 " --> pdb=" O ASP A4671 " (cutoff:3.500A) Processing helix chain 'A' and resid 4683 through 4695 removed outlier: 3.539A pdb=" N GLN A4695 " --> pdb=" O LEU A4691 " (cutoff:3.500A) Processing helix chain 'A' and resid 4701 through 4706 removed outlier: 4.140A pdb=" N HIS A4706 " --> pdb=" O ASN A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4737 removed outlier: 4.374A pdb=" N GLN A4737 " --> pdb=" O SER A4734 " (cutoff:3.500A) Processing helix chain 'B' and resid 4594 through 4599 removed outlier: 3.663A pdb=" N ALA B4598 " --> pdb=" O ASN B4594 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B4599 " --> pdb=" O CYS B4595 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4594 through 4599' Processing helix chain 'B' and resid 4600 through 4602 No H-bonds generated for 'chain 'B' and resid 4600 through 4602' Processing helix chain 'B' and resid 4641 through 4646 Processing helix chain 'B' and resid 4647 through 4649 No H-bonds generated for 'chain 'B' and resid 4647 through 4649' Processing helix chain 'B' and resid 4651 through 4655 removed outlier: 4.212A pdb=" N GLN B4654 " --> pdb=" O LEU B4651 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4675 removed outlier: 3.908A pdb=" N MET B4675 " --> pdb=" O ASP B4671 " (cutoff:3.500A) Processing helix chain 'B' and resid 4683 through 4695 removed outlier: 3.540A pdb=" N GLN B4695 " --> pdb=" O LEU B4691 " (cutoff:3.500A) Processing helix chain 'B' and resid 4701 through 4706 removed outlier: 4.139A pdb=" N HIS B4706 " --> pdb=" O ASN B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4737 removed outlier: 4.374A pdb=" N GLN B4737 " --> pdb=" O SER B4734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4382 through 4386 Processing sheet with id=AA2, first strand: chain 'A' and resid 4414 through 4417 Processing sheet with id=AA3, first strand: chain 'A' and resid 4447 through 4449 Processing sheet with id=AA4, first strand: chain 'A' and resid 4508 through 4512 removed outlier: 3.914A pdb=" N LEU A4490 " --> pdb=" O ILE A4501 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A4471 " --> pdb=" O LEU A4458 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A4570 " --> pdb=" O GLU A4460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 4718 through 4724 removed outlier: 5.618A pdb=" N TYR A4719 " --> pdb=" O PHE A4747 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A4747 " --> pdb=" O TYR A4719 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A4721 " --> pdb=" O GLY A4745 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY A4745 " --> pdb=" O ALA A4721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 4753 through 4754 Processing sheet with id=AA7, first strand: chain 'A' and resid 4768 through 4769 Processing sheet with id=AA8, first strand: chain 'A' and resid 4781 through 4782 removed outlier: 3.614A pdb=" N CYS A4789 " --> pdb=" O PHE A4782 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4414 through 4417 Processing sheet with id=AB1, first strand: chain 'B' and resid 4447 through 4449 Processing sheet with id=AB2, first strand: chain 'B' and resid 4508 through 4512 removed outlier: 3.915A pdb=" N LEU B4490 " --> pdb=" O ILE B4501 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B4471 " --> pdb=" O LEU B4458 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B4570 " --> pdb=" O GLU B4460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4718 through 4724 removed outlier: 5.619A pdb=" N TYR B4719 " --> pdb=" O PHE B4747 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE B4747 " --> pdb=" O TYR B4719 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B4721 " --> pdb=" O GLY B4745 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY B4745 " --> pdb=" O ALA B4721 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4753 through 4754 Processing sheet with id=AB5, first strand: chain 'B' and resid 4768 through 4769 Processing sheet with id=AB6, first strand: chain 'B' and resid 4781 through 4782 removed outlier: 3.615A pdb=" N CYS B4789 " --> pdb=" O PHE B4782 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 456 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: 2.32 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.45: 1818 1.45 - 1.57: 3579 1.57 - 1.70: 1 1.70 - 1.83: 100 Bond restraints: 6594 Sorted by residual: bond pdb=" CA THR A4740 " pdb=" C THR A4740 " ideal model delta sigma weight residual 1.523 1.605 -0.081 1.34e-02 5.57e+03 3.68e+01 bond pdb=" N VAL B4659 " pdb=" CA VAL B4659 " ideal model delta sigma weight residual 1.454 1.495 -0.041 7.70e-03 1.69e+04 2.78e+01 bond pdb=" N VAL A4659 " pdb=" CA VAL A4659 " ideal model delta sigma weight residual 1.454 1.495 -0.040 7.70e-03 1.69e+04 2.73e+01 bond pdb=" N LYS A4609 " pdb=" CA LYS A4609 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.40e-03 1.83e+04 2.23e+01 bond pdb=" N LYS B4609 " pdb=" CA LYS B4609 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.16e+01 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 95.07 - 102.88: 68 102.88 - 110.68: 2163 110.68 - 118.49: 3253 118.49 - 126.30: 3412 126.30 - 134.11: 126 Bond angle restraints: 9022 Sorted by residual: angle pdb=" N VAL A4741 " pdb=" CA VAL A4741 " pdb=" C VAL A4741 " ideal model delta sigma weight residual 109.51 95.48 14.03 1.43e+00 4.89e-01 9.62e+01 angle pdb=" N ASN A4739 " pdb=" CA ASN A4739 " pdb=" C ASN A4739 " ideal model delta sigma weight residual 113.23 102.85 10.38 1.24e+00 6.50e-01 7.01e+01 angle pdb=" C VAL B4392 " pdb=" N GLU B4393 " pdb=" CA GLU B4393 " ideal model delta sigma weight residual 122.84 112.46 10.38 1.30e+00 5.92e-01 6.37e+01 angle pdb=" C VAL A4392 " pdb=" N GLU A4393 " pdb=" CA GLU A4393 " ideal model delta sigma weight residual 122.84 112.46 10.38 1.30e+00 5.92e-01 6.37e+01 angle pdb=" N GLY B4410 " pdb=" CA GLY B4410 " pdb=" C GLY B4410 " ideal model delta sigma weight residual 114.69 105.23 9.46 1.19e+00 7.06e-01 6.31e+01 ... (remaining 9017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 3701 18.76 - 37.52: 309 37.52 - 56.28: 139 56.28 - 75.04: 52 75.04 - 93.80: 18 Dihedral angle restraints: 4219 sinusoidal: 1853 harmonic: 2366 Sorted by residual: dihedral pdb=" CB CYS B4713 " pdb=" SG CYS B4713 " pdb=" SG CYS B4746 " pdb=" CB CYS B4746 " ideal model delta sinusoidal sigma weight residual -86.00 -162.50 76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A4713 " pdb=" SG CYS A4713 " pdb=" SG CYS A4746 " pdb=" CB CYS A4746 " ideal model delta sinusoidal sigma weight residual -86.00 -162.49 76.49 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B4682 " pdb=" SG CYS B4682 " pdb=" SG CYS B4709 " pdb=" CB CYS B4709 " ideal model delta sinusoidal sigma weight residual 93.00 164.03 -71.03 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 950 0.169 - 0.338: 66 0.338 - 0.507: 6 0.507 - 0.676: 2 0.676 - 0.845: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.63e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.58e+02 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 1.63 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 1023 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.336 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG D 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.335 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG C 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.215 2.00e-02 2.50e+03 1.77e-01 3.92e+02 pdb=" C7 NAG D 2 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 168 2.67 - 3.22: 5794 3.22 - 3.78: 9234 3.78 - 4.34: 12507 4.34 - 4.90: 20315 Nonbonded interactions: 48018 Sorted by model distance: nonbonded pdb=" O ASN B4739 " pdb=" CG2 THR B4740 " model vdw 2.107 3.460 nonbonded pdb=" O ASN A4739 " pdb=" CG2 THR A4740 " model vdw 2.191 3.460 nonbonded pdb=" OH TYR B4450 " pdb=" OD1 ASP B4600 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A4450 " pdb=" OD1 ASP A4600 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR B4575 " pdb=" O ASP B4582 " model vdw 2.335 2.440 ... (remaining 48013 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' selection = chain 'B' } ncs_group { reference = 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 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: 7.930 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: 25.530 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.260 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 6594 Z= 0.556 Angle : 1.465 16.723 9022 Z= 0.959 Chirality : 0.102 0.845 1026 Planarity : 0.016 0.292 1168 Dihedral : 18.424 93.801 2582 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.77 % Favored : 90.98 % Rotamer: Outliers : 14.67 % Allowed : 5.13 % Favored : 80.20 % Cbeta Deviations : 0.53 % 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: -1.90 (0.29), residues: 798 helix: 0.55 (0.64), residues: 78 sheet: -0.74 (0.39), residues: 190 loop : -1.85 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B4377 HIS 0.003 0.001 HIS A4425 PHE 0.021 0.002 PHE B4652 TYR 0.018 0.002 TYR B4551 ARG 0.011 0.001 ARG A4564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 75 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4688 TYR cc_start: 0.8198 (t80) cc_final: 0.7825 (t80) REVERT: A 4792 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 4695 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6030 (mm110) outliers start: 103 outliers final: 31 residues processed: 155 average time/residue: 0.1922 time to fit residues: 38.4630 Evaluate side-chains 85 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 52 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4385 THR Chi-restraints excluded: chain A residue 4391 THR Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4409 ASN Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4473 ILE Chi-restraints excluded: chain A residue 4476 TYR Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4691 LEU Chi-restraints excluded: chain A residue 4699 LEU Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4782 PHE Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4407 CYS Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4486 CYS Chi-restraints excluded: chain B residue 4489 THR Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4609 LYS Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4782 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4475 ASN A4720 GLN ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6594 Z= 0.262 Angle : 0.743 6.989 9022 Z= 0.373 Chirality : 0.050 0.221 1026 Planarity : 0.005 0.057 1168 Dihedral : 11.612 69.183 1244 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.70 % Allowed : 13.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.30), residues: 798 helix: 0.53 (0.63), residues: 80 sheet: -0.43 (0.38), residues: 194 loop : -1.58 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A4377 HIS 0.005 0.001 HIS A4716 PHE 0.011 0.001 PHE A4782 TYR 0.015 0.001 TYR A4688 ARG 0.002 0.000 ARG B4559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 51 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 79 average time/residue: 0.2164 time to fit residues: 22.1494 Evaluate side-chains 62 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4391 THR Chi-restraints excluded: chain A residue 4409 ASN Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4477 HIS Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4489 THR Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4695 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4720 GLN ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6594 Z= 0.206 Angle : 0.648 6.048 9022 Z= 0.326 Chirality : 0.047 0.194 1026 Planarity : 0.005 0.071 1168 Dihedral : 8.895 62.629 1206 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 3.56 % Allowed : 14.81 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.30), residues: 798 helix: 0.68 (0.62), residues: 80 sheet: -0.19 (0.39), residues: 182 loop : -1.28 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4424 HIS 0.009 0.001 HIS A4611 PHE 0.015 0.002 PHE B4782 TYR 0.021 0.001 TYR A4476 ARG 0.019 0.001 ARG B4415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4792 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8618 (pp) REVERT: B 4695 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6089 (mm110) outliers start: 25 outliers final: 14 residues processed: 73 average time/residue: 0.2125 time to fit residues: 20.3257 Evaluate side-chains 61 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4477 HIS Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4695 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4720 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6594 Z= 0.292 Angle : 0.677 5.736 9022 Z= 0.342 Chirality : 0.049 0.195 1026 Planarity : 0.005 0.064 1168 Dihedral : 7.652 55.236 1201 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.99 % Allowed : 17.66 % Favored : 79.34 % 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: -1.05 (0.30), residues: 798 helix: 0.39 (0.62), residues: 84 sheet: 0.06 (0.40), residues: 174 loop : -1.19 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B4376 HIS 0.006 0.001 HIS A4716 PHE 0.019 0.002 PHE B4782 TYR 0.022 0.002 TYR B4551 ARG 0.005 0.000 ARG B4559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4792 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8658 (pp) REVERT: B 4695 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6763 (mm-40) outliers start: 21 outliers final: 14 residues processed: 61 average time/residue: 0.2107 time to fit residues: 17.0832 Evaluate side-chains 56 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.7471 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6594 Z= 0.208 Angle : 0.605 5.391 9022 Z= 0.303 Chirality : 0.046 0.148 1026 Planarity : 0.004 0.045 1168 Dihedral : 6.722 56.788 1195 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.13 % Allowed : 20.09 % Favored : 76.78 % 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: -1.01 (0.30), residues: 798 helix: 0.46 (0.62), residues: 84 sheet: 0.09 (0.40), residues: 174 loop : -1.17 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B4424 HIS 0.005 0.001 HIS A4611 PHE 0.014 0.001 PHE A4782 TYR 0.016 0.001 TYR A4476 ARG 0.003 0.000 ARG B4559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 42 time to evaluate : 0.688 Fit side-chains REVERT: A 4525 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7808 (ttmm) REVERT: A 4791 CYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6765 (t) REVERT: A 4792 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8636 (pp) REVERT: B 4695 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6920 (mm-40) REVERT: B 4792 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8798 (pp) outliers start: 22 outliers final: 9 residues processed: 58 average time/residue: 0.1872 time to fit residues: 14.8511 Evaluate side-chains 53 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4525 LYS Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6594 Z= 0.254 Angle : 0.629 8.190 9022 Z= 0.314 Chirality : 0.046 0.151 1026 Planarity : 0.004 0.042 1168 Dihedral : 6.204 55.308 1190 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 4.70 % Allowed : 18.66 % Favored : 76.64 % 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: -0.80 (0.30), residues: 798 helix: 1.54 (0.66), residues: 72 sheet: 0.20 (0.40), residues: 174 loop : -1.12 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4424 HIS 0.010 0.001 HIS A4477 PHE 0.014 0.001 PHE B4782 TYR 0.015 0.001 TYR A4476 ARG 0.005 0.001 ARG B4415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 40 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4525 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7986 (ttmm) REVERT: A 4753 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8305 (ppp) REVERT: A 4791 CYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6874 (t) REVERT: A 4792 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8660 (pp) REVERT: B 4646 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 4695 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6989 (mm-40) REVERT: B 4792 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8836 (pp) outliers start: 33 outliers final: 11 residues processed: 65 average time/residue: 0.2166 time to fit residues: 18.9400 Evaluate side-chains 57 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4509 MET Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4525 LYS Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4646 LEU Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 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: 0.7525 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6594 Z= 0.244 Angle : 0.627 9.790 9022 Z= 0.314 Chirality : 0.046 0.174 1026 Planarity : 0.004 0.041 1168 Dihedral : 6.091 55.961 1190 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 3.28 % Allowed : 19.52 % Favored : 77.21 % 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 (0.30), residues: 798 helix: 1.58 (0.66), residues: 72 sheet: 0.09 (0.39), residues: 186 loop : -1.10 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4424 HIS 0.004 0.001 HIS B4716 PHE 0.013 0.001 PHE B4782 TYR 0.014 0.001 TYR A4476 ARG 0.005 0.000 ARG B4415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7128 (ptm) REVERT: A 4611 HIS cc_start: 0.4704 (OUTLIER) cc_final: 0.4286 (p90) REVERT: A 4791 CYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6883 (t) REVERT: A 4792 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8666 (pp) REVERT: B 4646 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 4695 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7154 (mm-40) REVERT: B 4792 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8799 (pp) outliers start: 23 outliers final: 11 residues processed: 58 average time/residue: 0.1943 time to fit residues: 15.2548 Evaluate side-chains 58 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4509 MET Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4646 LEU Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7521 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6594 Z= 0.215 Angle : 0.613 5.753 9022 Z= 0.307 Chirality : 0.045 0.165 1026 Planarity : 0.004 0.040 1168 Dihedral : 5.960 56.304 1190 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.85 % Allowed : 19.80 % Favored : 77.35 % 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: -0.74 (0.30), residues: 798 helix: 1.59 (0.66), residues: 72 sheet: 0.22 (0.40), residues: 174 loop : -1.07 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4424 HIS 0.003 0.001 HIS B4716 PHE 0.013 0.001 PHE B4782 TYR 0.013 0.001 TYR A4476 ARG 0.004 0.000 ARG B4415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 41 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7137 (ptm) REVERT: A 4753 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8273 (ppp) REVERT: A 4791 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6893 (t) REVERT: A 4792 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8669 (pp) REVERT: B 4695 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: B 4792 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8794 (pp) outliers start: 20 outliers final: 11 residues processed: 56 average time/residue: 0.2065 time to fit residues: 15.7194 Evaluate side-chains 57 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4509 MET Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7509 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.195 Angle : 0.613 11.343 9022 Z= 0.302 Chirality : 0.045 0.155 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.770 56.769 1190 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.71 % Allowed : 19.80 % Favored : 77.49 % 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: -0.71 (0.30), residues: 798 helix: 1.62 (0.66), residues: 72 sheet: 0.25 (0.40), residues: 174 loop : -1.06 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4426 HIS 0.005 0.001 HIS A4505 PHE 0.013 0.001 PHE B4782 TYR 0.011 0.001 TYR A4476 ARG 0.003 0.000 ARG B4415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7376 (ptp) REVERT: A 4753 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8252 (ppp) REVERT: A 4791 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6926 (t) REVERT: A 4792 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 4695 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7320 (mm-40) REVERT: B 4792 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8782 (pp) outliers start: 19 outliers final: 11 residues processed: 55 average time/residue: 0.2963 time to fit residues: 21.7971 Evaluate side-chains 58 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4509 MET Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4428 CYS Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7532 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6594 Z= 0.222 Angle : 0.611 8.005 9022 Z= 0.305 Chirality : 0.045 0.149 1026 Planarity : 0.004 0.039 1168 Dihedral : 5.712 57.438 1190 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.71 % Allowed : 19.23 % Favored : 78.06 % 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: -0.64 (0.30), residues: 798 helix: 1.98 (0.67), residues: 68 sheet: 0.33 (0.40), residues: 174 loop : -1.04 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4424 HIS 0.004 0.001 HIS B4716 PHE 0.013 0.001 PHE B4782 TYR 0.012 0.001 TYR A4476 ARG 0.003 0.000 ARG B4415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (ptp) REVERT: A 4753 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8235 (ppp) REVERT: A 4792 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8673 (pp) REVERT: B 4695 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7390 (mm-40) REVERT: B 4792 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8791 (pp) outliers start: 19 outliers final: 12 residues processed: 53 average time/residue: 0.2071 time to fit residues: 14.9760 Evaluate side-chains 56 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4509 MET Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4583 ASP Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4428 CYS Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.097924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072104 restraints weight = 15686.240| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.76 r_work: 0.3057 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6594 Z= 0.219 Angle : 0.613 10.137 9022 Z= 0.305 Chirality : 0.045 0.187 1026 Planarity : 0.004 0.039 1168 Dihedral : 5.685 58.686 1190 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % Favored : 78.21 % 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: -0.66 (0.30), residues: 798 helix: 1.59 (0.66), residues: 72 sheet: 0.31 (0.40), residues: 174 loop : -1.03 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4424 HIS 0.004 0.001 HIS A4611 PHE 0.018 0.001 PHE A4674 TYR 0.011 0.001 TYR A4551 ARG 0.004 0.000 ARG B4415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.93 seconds wall clock time: 37 minutes 5.65 seconds (2225.65 seconds total)