Starting phenix.real_space_refine (version: dev) on Sat Feb 18 09:05:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/02_2023/8d43_27173.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7763 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6952 Classifications: {'peptide': 862} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 801} Chain breaks: 2 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.67 Number of scatterers: 7763 At special positions: 0 Unit cell: (70.62, 88.81, 116.63, 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 35 16.00 O 1454 8.00 N 1346 7.00 C 4926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 112 " distance=2.03 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 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 97 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 22.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.624A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.799A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.517A pdb=" N GLY A 565 " --> pdb=" O HIS A 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 566 " --> pdb=" O TYR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 571 through 592 removed outlier: 4.340A pdb=" N GLY A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.689A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.875A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 685 through 689 removed outlier: 3.912A pdb=" N LEU A 689 " --> pdb=" O PRO A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.597A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.203A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.113A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.812A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.390A pdb=" N HIS B 29 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.830A pdb=" N MET A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 321 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 645 removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 599 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP A 615 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 601 " --> pdb=" O TRP A 615 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 600 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 463 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TRP A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 465 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.941A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.129A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 916 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 840 through 846 removed outlier: 3.596A pdb=" N TRP A 939 " --> pdb=" O SER A 874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 77 273 hydrogen bonds defined for protein. 714 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: 3.07 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2400 1.33 - 1.46: 1518 1.46 - 1.58: 4014 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7985 Sorted by residual: bond pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.22e-02 6.72e+03 7.99e+00 bond pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 1.525 1.493 0.031 1.28e-02 6.10e+03 5.99e+00 bond pdb=" C CYS B 70 " pdb=" O CYS B 70 " ideal model delta sigma weight residual 1.240 1.214 0.025 1.16e-02 7.43e+03 4.68e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.435 1.411 0.024 1.10e-02 8.26e+03 4.66e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.522 1.506 0.016 8.30e-03 1.45e+04 3.58e+00 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.95: 209 104.95 - 112.32: 3872 112.32 - 119.69: 2823 119.69 - 127.05: 3824 127.05 - 134.42: 145 Bond angle restraints: 10873 Sorted by residual: angle pdb=" N SER A 506 " pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 108.96 98.00 10.96 1.59e+00 3.96e-01 4.75e+01 angle pdb=" C ARG A 110 " pdb=" N PRO A 111 " pdb=" CA PRO A 111 " ideal model delta sigma weight residual 119.76 113.52 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N ASP B 101 " pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 108.20 97.58 10.62 1.71e+00 3.42e-01 3.86e+01 angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 115.64 108.38 7.26 1.46e+00 4.69e-01 2.48e+01 angle pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta sigma weight residual 110.39 117.49 -7.10 1.61e+00 3.86e-01 1.94e+01 ... (remaining 10868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 4192 23.57 - 47.14: 442 47.14 - 70.71: 73 70.71 - 94.28: 13 94.28 - 117.84: 1 Dihedral angle restraints: 4721 sinusoidal: 1947 harmonic: 2774 Sorted by residual: dihedral pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual 122.80 136.80 -14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C TRP A 503 " pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual -122.60 -133.76 11.16 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" C3 MAN C 4 " pdb=" O3 MAN C 4 " ideal model delta sinusoidal sigma weight residual -173.26 -55.42 -117.84 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 4718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1067 0.102 - 0.205: 81 0.205 - 0.307: 5 0.307 - 0.410: 1 0.410 - 0.512: 1 Chirality restraints: 1155 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 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.22e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.14e+01 ... (remaining 1152 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.143 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" C7 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 503 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 504 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 826 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 827 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 827 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 827 " 0.032 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 1750 2.78 - 3.49: 10223 3.49 - 4.19: 20876 4.19 - 4.90: 35979 Nonbonded interactions: 68829 Sorted by model distance: nonbonded pdb=" OD2 ASP B 57 " pdb="CA CA B 602 " model vdw 1.371 2.510 nonbonded pdb=" OE2 GLU B 105 " pdb="CA CA B 601 " model vdw 2.091 2.510 nonbonded pdb=" OD1 ASP B 94 " pdb="CA CA B 601 " model vdw 2.112 2.510 nonbonded pdb=" OD1 ASP B 53 " pdb="CA CA B 602 " model vdw 2.177 2.510 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.194 2.510 ... (remaining 68824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4926 2.51 5 N 1346 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 9.470 Check model and map are aligned: 0.130 Process input model: 25.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7985 Z= 0.272 Angle : 0.835 10.960 10873 Z= 0.484 Chirality : 0.057 0.512 1155 Planarity : 0.007 0.119 1426 Dihedral : 18.398 117.844 2933 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 5.48 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.97 % 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 (0.26), residues: 954 helix: -1.16 (0.40), residues: 160 sheet: -0.25 (0.33), residues: 223 loop : -1.24 (0.26), residues: 571 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 65 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 13 residues processed: 110 average time/residue: 0.8472 time to fit residues: 101.5552 Evaluate side-chains 47 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.1503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS A 934 ASN A 942 HIS B 27 ASN B 28 HIS B 29 HIS B 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0320 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7985 Z= 0.239 Angle : 0.682 10.311 10873 Z= 0.343 Chirality : 0.046 0.173 1155 Planarity : 0.006 0.063 1426 Dihedral : 6.855 96.219 1096 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 7.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -1.14 (0.27), residues: 954 helix: -0.52 (0.37), residues: 162 sheet: -0.28 (0.33), residues: 230 loop : -1.01 (0.27), residues: 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 39 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 23 residues processed: 96 average time/residue: 0.9078 time to fit residues: 94.7929 Evaluate side-chains 55 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 32 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.8281 time to fit residues: 4.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 670 GLN A 676 HIS A 804 GLN A 919 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0925 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 7985 Z= 0.288 Angle : 0.765 18.259 10873 Z= 0.373 Chirality : 0.048 0.181 1155 Planarity : 0.007 0.059 1426 Dihedral : 7.132 96.572 1096 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.08 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -1.30 (0.27), residues: 954 helix: -0.73 (0.37), residues: 162 sheet: -0.51 (0.33), residues: 235 loop : -1.03 (0.27), residues: 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 44 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 25 residues processed: 94 average time/residue: 0.8765 time to fit residues: 90.1275 Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.3661 time to fit residues: 3.0909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1631 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 7985 Z= 0.351 Angle : 0.900 18.692 10873 Z= 0.448 Chirality : 0.052 0.175 1155 Planarity : 0.008 0.074 1426 Dihedral : 7.674 90.227 1096 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.49 % Favored : 91.40 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -1.99 (0.26), residues: 954 helix: -1.42 (0.34), residues: 166 sheet: -0.54 (0.34), residues: 230 loop : -1.66 (0.26), residues: 558 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 52 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 21 residues processed: 101 average time/residue: 0.8180 time to fit residues: 90.7110 Evaluate side-chains 66 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.0740 time to fit residues: 1.5675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2117 moved from start: 0.8346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 7985 Z= 0.347 Angle : 0.879 19.016 10873 Z= 0.438 Chirality : 0.052 0.301 1155 Planarity : 0.008 0.069 1426 Dihedral : 7.858 92.157 1096 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.82 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.21 (0.25), residues: 954 helix: -1.57 (0.33), residues: 170 sheet: -0.51 (0.35), residues: 212 loop : -1.86 (0.25), residues: 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 51 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 101 average time/residue: 0.7522 time to fit residues: 84.1189 Evaluate side-chains 75 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 48 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.0788 time to fit residues: 1.6012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2182 moved from start: 0.8926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 7985 Z= 0.245 Angle : 0.732 16.768 10873 Z= 0.357 Chirality : 0.047 0.216 1155 Planarity : 0.006 0.052 1426 Dihedral : 7.332 92.581 1096 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.14 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 (0.26), residues: 954 helix: -0.97 (0.36), residues: 169 sheet: -0.38 (0.35), residues: 213 loop : -1.79 (0.25), residues: 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 46 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 27 residues processed: 81 average time/residue: 0.7212 time to fit residues: 65.0437 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 40 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.8218 time to fit residues: 3.9554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2689 moved from start: 1.0280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 7985 Z= 0.312 Angle : 0.825 14.818 10873 Z= 0.417 Chirality : 0.050 0.208 1155 Planarity : 0.007 0.061 1426 Dihedral : 7.526 92.977 1096 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.91 % Favored : 90.99 % Rotamer Outliers : 5.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -2.03 (0.26), residues: 954 helix: -1.28 (0.36), residues: 167 sheet: -0.52 (0.36), residues: 212 loop : -1.74 (0.25), residues: 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 48 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 89 average time/residue: 0.9510 time to fit residues: 92.6429 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.6276 time to fit residues: 2.5662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.0060 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 72 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2650 moved from start: 1.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7985 Z= 0.209 Angle : 0.756 13.458 10873 Z= 0.362 Chirality : 0.046 0.193 1155 Planarity : 0.006 0.055 1426 Dihedral : 6.952 93.234 1096 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.92 % Favored : 92.98 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -1.87 (0.26), residues: 954 helix: -0.68 (0.38), residues: 165 sheet: -0.58 (0.35), residues: 220 loop : -1.74 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 54 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 86 average time/residue: 0.8113 time to fit residues: 76.7947 Evaluate side-chains 68 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.0747 time to fit residues: 1.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 26 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2692 moved from start: 1.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 7985 Z= 0.192 Angle : 0.708 15.374 10873 Z= 0.342 Chirality : 0.045 0.172 1155 Planarity : 0.006 0.058 1426 Dihedral : 6.712 94.239 1096 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.24 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 (0.26), residues: 954 helix: -0.49 (0.38), residues: 166 sheet: -0.44 (0.35), residues: 219 loop : -1.64 (0.25), residues: 569 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 23 residues processed: 73 average time/residue: 0.8407 time to fit residues: 67.6431 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 1.3625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3199 moved from start: 1.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 7985 Z= 0.276 Angle : 0.856 16.607 10873 Z= 0.423 Chirality : 0.049 0.202 1155 Planarity : 0.008 0.139 1426 Dihedral : 6.956 92.680 1096 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.70 % Favored : 91.09 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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: -1.85 (0.26), residues: 954 helix: -0.88 (0.38), residues: 164 sheet: -0.42 (0.36), residues: 218 loop : -1.71 (0.26), residues: 572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 97 average time/residue: 0.8926 time to fit residues: 94.5255 Evaluate side-chains 72 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.1213 time to fit residues: 1.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 719 HIS A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.283467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.269155 restraints weight = 9490.003| |-----------------------------------------------------------------------------| r_work (start): 0.4835 rms_B_bonded: 1.52 r_work: 0.4781 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4689 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3546 moved from start: 1.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 7985 Z= 0.257 Angle : 0.801 13.783 10873 Z= 0.389 Chirality : 0.047 0.262 1155 Planarity : 0.006 0.057 1426 Dihedral : 6.737 93.109 1096 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.13 % Favored : 92.77 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 (0.26), residues: 954 helix: -0.54 (0.39), residues: 164 sheet: -0.26 (0.35), residues: 217 loop : -1.70 (0.25), residues: 573 =============================================================================== Job complete usr+sys time: 2697.84 seconds wall clock time: 49 minutes 18.87 seconds (2958.87 seconds total)