Starting phenix.real_space_refine on Wed Feb 14 05:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty6_26167/02_2024/7ty6_26167_updated.pdb" } resolution = 2.98 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= -0.002 sd= 0.033 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 P 2 5.49 5 S 44 5.16 5 C 5824 2.51 5 N 1320 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 Chain: "B" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 9.14, per 1000 atoms: 1.05 Number of scatterers: 8672 At special positions: 0 Unit cell: (112.98, 95.764, 83.928, 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) S 44 16.00 P 2 15.00 O 1482 8.00 N 1320 7.00 C 5824 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 66.7% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 380 through 400 Proline residue: A 391 - end of helix removed outlier: 5.171A pdb=" N LEU A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 430 removed outlier: 3.768A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 437 through 454 Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 486 through 506 removed outlier: 3.586A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 518 through 546 removed outlier: 3.559A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 609 through 623 Processing helix chain 'A' and resid 661 through 689 removed outlier: 5.122A pdb=" N ALA A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.650A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 761 through 773 Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.294A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.836A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 removed outlier: 3.589A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 856 through 871 Proline residue: A 860 - end of helix removed outlier: 3.512A pdb=" N LEU A 863 " --> pdb=" O PRO A 860 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'B' and resid 380 through 400 Proline residue: B 391 - end of helix removed outlier: 5.171A pdb=" N LEU B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 430 removed outlier: 3.769A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 437 through 454 Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 486 through 506 removed outlier: 3.585A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 518 through 546 removed outlier: 3.548A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 609 through 623 Processing helix chain 'B' and resid 661 through 689 removed outlier: 5.126A pdb=" N ALA B 668 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Proline residue: B 670 - end of helix Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.648A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.300A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.835A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 812 removed outlier: 3.592A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 826 No H-bonds generated for 'chain 'B' and resid 823 through 826' Processing helix chain 'B' and resid 830 through 852 Processing helix chain 'B' and resid 856 through 871 Proline residue: B 860 - end of helix Proline residue: B 868 - end of helix Processing helix chain 'B' and resid 874 through 877 No H-bonds generated for 'chain 'B' and resid 874 through 877' Processing helix chain 'B' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'A' and resid 739 through 741 removed outlier: 3.877A pdb=" N GLU A 755 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 739 through 741 removed outlier: 3.863A pdb=" N GLU B 755 " --> pdb=" O VAL B 740 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1308 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: 2.31 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1396 1.33 - 1.45: 2166 1.45 - 1.57: 5202 1.57 - 1.70: 8 1.70 - 1.82: 70 Bond restraints: 8842 Sorted by residual: bond pdb=" CAL 4DS B2204 " pdb=" CAM 4DS B2204 " ideal model delta sigma weight residual 1.770 1.513 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" CAL 4DS A2204 " pdb=" CAM 4DS A2204 " ideal model delta sigma weight residual 1.770 1.514 0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" CAG 4DS A2204 " pdb=" NAZ 4DS A2204 " ideal model delta sigma weight residual 1.618 1.411 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAG 4DS B2204 " pdb=" NAZ 4DS B2204 " ideal model delta sigma weight residual 1.618 1.415 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAD 4DS B2204 " pdb=" SAB 4DS B2204 " ideal model delta sigma weight residual 1.617 1.437 0.180 2.00e-02 2.50e+03 8.08e+01 ... (remaining 8837 not shown) Histogram of bond angle deviations from ideal: 99.14 - 114.48: 5535 114.48 - 129.82: 6475 129.82 - 145.15: 42 145.15 - 160.49: 0 160.49 - 175.83: 2 Bond angle restraints: 12054 Sorted by residual: angle pdb=" NAS 4DS A2204 " pdb=" CAT 4DS A2204 " pdb=" SAU 4DS A2204 " ideal model delta sigma weight residual 180.00 125.79 54.21 3.00e+00 1.11e-01 3.27e+02 angle pdb=" NAS 4DS B2204 " pdb=" CAT 4DS B2204 " pdb=" SAU 4DS B2204 " ideal model delta sigma weight residual 180.00 126.11 53.89 3.00e+00 1.11e-01 3.23e+02 angle pdb=" N PHE B 608 " pdb=" CA PHE B 608 " pdb=" C PHE B 608 " ideal model delta sigma weight residual 112.97 103.92 9.05 1.06e+00 8.90e-01 7.29e+01 angle pdb=" N LYS B 430 " pdb=" CA LYS B 430 " pdb=" C LYS B 430 " ideal model delta sigma weight residual 111.28 118.67 -7.39 1.09e+00 8.42e-01 4.59e+01 angle pdb=" N LYS A 430 " pdb=" CA LYS A 430 " pdb=" C LYS A 430 " ideal model delta sigma weight residual 111.82 119.12 -7.30 1.16e+00 7.43e-01 3.97e+01 ... (remaining 12049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 5253 21.93 - 43.86: 277 43.86 - 65.79: 82 65.79 - 87.72: 20 87.72 - 109.65: 16 Dihedral angle restraints: 5648 sinusoidal: 2664 harmonic: 2984 Sorted by residual: dihedral pdb=" C ASN B 554 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " pdb=" CB ASN B 554 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C ASN A 554 " pdb=" N ASN A 554 " pdb=" CA ASN A 554 " pdb=" CB ASN A 554 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sinusoidal sigma weight residual 175.11 65.46 109.65 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 722 0.067 - 0.135: 573 0.135 - 0.202: 135 0.202 - 0.269: 5 0.269 - 0.337: 3 Chirality restraints: 1438 Sorted by residual: 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 -2.06 -0.34 2.00e-02 2.50e+03 2.83e+02 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 -2.21 -0.19 2.00e-02 2.50e+03 9.31e+01 chirality pdb=" CA ASN B 554 " pdb=" N ASN B 554 " pdb=" C ASN B 554 " pdb=" CB ASN B 554 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1435 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG C 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.327 2.00e-02 2.50e+03 2.78e-01 9.68e+02 pdb=" C7 NAG D 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAP 4DS A2204 " 0.111 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" CAT 4DS A2204 " 0.285 2.00e-02 2.50e+03 pdb=" NAS 4DS A2204 " -0.309 2.00e-02 2.50e+03 pdb=" SAU 4DS A2204 " -0.087 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2006 2.87 - 3.38: 9559 3.38 - 3.89: 14908 3.89 - 4.39: 17828 4.39 - 4.90: 29034 Nonbonded interactions: 73335 Sorted by model distance: nonbonded pdb=" O LEU B 863 " pdb=" OG1 THR B 866 " model vdw 2.366 2.440 nonbonded pdb=" O LEU A 863 " pdb=" OG1 THR A 866 " model vdw 2.381 2.440 nonbonded pdb=" O THR A 686 " pdb=" OG SER A 690 " model vdw 2.396 2.440 nonbonded pdb=" O THR B 686 " pdb=" OG SER B 690 " model vdw 2.397 2.440 nonbonded pdb=" O THR A 727 " pdb=" OG SER A 731 " model vdw 2.448 2.440 ... (remaining 73330 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 369 through 650 or resid 652 through 891 or resid 2201 thr \ ough 2206)) selection = (chain 'B' and (resid 369 through 650 or resid 652 through 891 or resid 2201 thr \ ough 2206)) } 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=0.50 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: 9.200 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: 7.590 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.490 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.015 0.257 8842 Z= 0.982 Angle : 1.930 54.208 12054 Z= 1.381 Chirality : 0.086 0.337 1438 Planarity : 0.016 0.291 1414 Dihedral : 16.120 109.651 3724 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.89 % Allowed : 4.89 % Favored : 94.22 % Cbeta Deviations : 0.21 % 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: -2.86 (0.21), residues: 1026 helix: -1.62 (0.16), residues: 692 sheet: None (None), residues: 0 loop : -2.17 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 492 HIS 0.005 0.002 HIS B 819 PHE 0.018 0.003 PHE B 675 TYR 0.013 0.003 TYR B 824 ARG 0.003 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 880 ASN cc_start: 0.9403 (t0) cc_final: 0.9154 (t0) REVERT: B 473 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8841 (tp30) REVERT: B 880 ASN cc_start: 0.9396 (t0) cc_final: 0.9152 (t0) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 1.3990 time to fit residues: 111.8717 Evaluate side-chains 51 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ARG Chi-restraints excluded: chain B residue 603 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 554 ASN A 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8842 Z= 0.215 Angle : 0.610 6.875 12054 Z= 0.295 Chirality : 0.040 0.218 1438 Planarity : 0.005 0.044 1414 Dihedral : 12.840 83.484 1822 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.67 % Allowed : 8.89 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1026 helix: 1.05 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 492 HIS 0.001 0.001 HIS B 703 PHE 0.017 0.001 PHE B 411 TYR 0.009 0.001 TYR A 519 ARG 0.002 0.001 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8819 (mp0) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 1.3080 time to fit residues: 70.2547 Evaluate side-chains 43 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 91 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN B 433 ASN B 554 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8842 Z= 0.160 Angle : 0.551 9.127 12054 Z= 0.262 Chirality : 0.038 0.159 1438 Planarity : 0.005 0.050 1414 Dihedral : 10.716 79.170 1814 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.11 % Allowed : 9.22 % Favored : 89.67 % 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: 1.26 (0.26), residues: 1026 helix: 1.80 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.29 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.001 0.000 HIS B 734 PHE 0.018 0.001 PHE A 719 TYR 0.012 0.001 TYR A 519 ARG 0.006 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9162 (m110) cc_final: 0.8954 (m110) REVERT: A 603 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.9087 (mpp-170) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.1523 time to fit residues: 67.6802 Evaluate side-chains 47 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 603 ARG Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8842 Z= 0.213 Angle : 0.556 11.873 12054 Z= 0.259 Chirality : 0.038 0.117 1438 Planarity : 0.005 0.051 1414 Dihedral : 9.918 80.321 1814 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.44 % Allowed : 8.67 % Favored : 89.89 % 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: 1.48 (0.27), residues: 1026 helix: 1.85 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 492 HIS 0.001 0.000 HIS B 703 PHE 0.014 0.001 PHE B 411 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.9277 (mmm) cc_final: 0.9027 (mmt) REVERT: A 721 MET cc_start: 0.8935 (mpp) cc_final: 0.8445 (mpp) outliers start: 13 outliers final: 5 residues processed: 51 average time/residue: 1.1557 time to fit residues: 64.1712 Evaluate side-chains 47 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN B 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8842 Z= 0.293 Angle : 0.597 10.225 12054 Z= 0.277 Chirality : 0.039 0.115 1438 Planarity : 0.005 0.051 1414 Dihedral : 9.607 80.254 1814 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.11 % Allowed : 8.67 % Favored : 90.22 % 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: 1.49 (0.27), residues: 1026 helix: 1.88 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 492 HIS 0.001 0.000 HIS B 834 PHE 0.012 0.001 PHE A 471 TYR 0.009 0.001 TYR A 519 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.9281 (mmm) cc_final: 0.9004 (mmt) REVERT: A 721 MET cc_start: 0.9065 (mpp) cc_final: 0.8633 (mpp) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 1.4093 time to fit residues: 73.3749 Evaluate side-chains 46 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8869 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8842 Z= 0.189 Angle : 0.549 9.946 12054 Z= 0.254 Chirality : 0.038 0.121 1438 Planarity : 0.005 0.051 1414 Dihedral : 9.166 80.270 1814 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.89 % Allowed : 9.22 % Favored : 89.89 % 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: 1.59 (0.27), residues: 1026 helix: 1.96 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 PHE 0.013 0.001 PHE B 411 TYR 0.011 0.001 TYR A 519 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.9286 (mmm) cc_final: 0.9021 (mmt) REVERT: A 721 MET cc_start: 0.9002 (mpp) cc_final: 0.8580 (mpp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.0093 time to fit residues: 55.5096 Evaluate side-chains 48 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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: 0.8863 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8842 Z= 0.179 Angle : 0.577 12.430 12054 Z= 0.260 Chirality : 0.038 0.127 1438 Planarity : 0.004 0.051 1414 Dihedral : 8.820 80.961 1814 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.89 % Allowed : 10.00 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 1026 helix: 2.02 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 PHE 0.012 0.001 PHE A 411 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.9292 (mmm) cc_final: 0.9026 (mmt) REVERT: A 721 MET cc_start: 0.9005 (mpp) cc_final: 0.8590 (mpp) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 1.3611 time to fit residues: 70.4211 Evaluate side-chains 48 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8856 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8842 Z= 0.174 Angle : 0.584 11.854 12054 Z= 0.260 Chirality : 0.038 0.134 1438 Planarity : 0.004 0.052 1414 Dihedral : 8.545 81.282 1814 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.78 % Allowed : 10.33 % Favored : 88.89 % 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: 1.77 (0.27), residues: 1026 helix: 2.08 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.97 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 PHE 0.012 0.001 PHE B 411 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.9268 (mmm) cc_final: 0.9066 (mmt) REVERT: A 721 MET cc_start: 0.9001 (mpp) cc_final: 0.8593 (mpp) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 1.0754 time to fit residues: 56.5237 Evaluate side-chains 50 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- 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: 0.8852 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8842 Z= 0.166 Angle : 0.565 12.283 12054 Z= 0.253 Chirality : 0.038 0.123 1438 Planarity : 0.004 0.051 1414 Dihedral : 8.355 81.362 1814 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.78 % Allowed : 10.56 % Favored : 88.67 % 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: 1.92 (0.27), residues: 1026 helix: 2.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 PHE 0.012 0.001 PHE B 411 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8994 (mpp) cc_final: 0.8584 (mpp) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 1.0603 time to fit residues: 57.0004 Evaluate side-chains 51 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.0070 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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: 0.8852 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8842 Z= 0.173 Angle : 0.586 12.551 12054 Z= 0.260 Chirality : 0.038 0.122 1438 Planarity : 0.004 0.051 1414 Dihedral : 8.296 81.945 1814 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.78 % Allowed : 10.67 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.27), residues: 1026 helix: 2.20 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.002 0.000 HIS A 547 PHE 0.012 0.001 PHE A 471 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG A 603 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8992 (mpp) cc_final: 0.8591 (mpp) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 1.0331 time to fit residues: 55.5873 Evaluate side-chains 52 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.2970 r_free = 0.2970 target = 0.056867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.046072 restraints weight = 66101.069| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 4.75 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8842 Z= 0.187 Angle : 0.575 12.532 12054 Z= 0.258 Chirality : 0.038 0.121 1438 Planarity : 0.005 0.050 1414 Dihedral : 8.240 82.724 1814 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.89 % Allowed : 10.56 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.27), residues: 1026 helix: 2.19 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.001 0.000 HIS A 547 PHE 0.012 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.003 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.69 seconds wall clock time: 42 minutes 17.55 seconds (2537.55 seconds total)