Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 17:00:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/08_2023/7ozu_13135_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 786} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.629 66.446 35.948 1.00 75.77 S ATOM 1733 SG CYS A 306 47.619 65.877 32.167 1.00 71.14 S ATOM 1765 SG CYS A 310 50.645 65.595 34.602 1.00 65.59 S ATOM 3132 SG CYS A 487 29.807 62.600 44.981 1.00 68.93 S ATOM 4385 SG CYS A 645 28.884 62.549 41.352 1.00 75.15 S ATOM 4391 SG CYS A 646 31.664 64.707 42.888 1.00 71.21 S Time building chain proxies: 4.84, per 1000 atoms: 0.58 Number of scatterers: 8408 At special positions: 0 Unit cell: (90.906, 94.242, 98.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 22 15.00 O 1638 8.00 N 1405 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 48.0% alpha, 9.8% beta 7 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.064A pdb=" N ASN A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.074A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 3.812A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.267A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.693A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.609A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.746A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.726A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 5.757A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 718 through 731 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.869A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 3.916A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.853A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.042A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.735A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 45 through 61 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.938A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.120A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.061A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1330 1.31 - 1.43: 2520 1.43 - 1.56: 4659 1.56 - 1.68: 46 1.68 - 1.81: 87 Bond restraints: 8642 Sorted by residual: bond pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.412 1.626 -0.214 1.50e-02 4.44e+03 2.03e+02 bond pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.529 1.346 0.183 1.50e-02 4.44e+03 1.50e+02 bond pdb=" C4' 7OK T 9 " pdb=" O4' 7OK T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" C4 7OK T 9 " pdb=" N4 7OK T 9 " ideal model delta sigma weight residual 1.261 1.439 -0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C2 7OK T 9 " pdb=" N3 7OK T 9 " ideal model delta sigma weight residual 1.494 1.329 0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 8637 not shown) Histogram of bond angle deviations from ideal: 92.05 - 100.44: 7 100.44 - 108.83: 635 108.83 - 117.22: 5515 117.22 - 125.60: 5493 125.60 - 133.99: 181 Bond angle restraints: 11831 Sorted by residual: angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" O5' A T 10 " ideal model delta sigma weight residual 104.00 92.05 11.95 1.50e+00 4.44e-01 6.34e+01 angle pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 112.00 122.08 -10.08 1.50e+00 4.44e-01 4.52e+01 angle pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 108.50 100.57 7.93 1.50e+00 4.44e-01 2.79e+01 angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" OP2 A T 10 " ideal model delta sigma weight residual 108.00 119.56 -11.56 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5' 7OK T 9 " pdb=" C4' 7OK T 9 " pdb=" C3' 7OK T 9 " ideal model delta sigma weight residual 116.00 110.24 5.76 1.50e+00 4.44e-01 1.48e+01 ... (remaining 11826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4624 17.03 - 34.06: 377 34.06 - 51.09: 48 51.09 - 68.12: 14 68.12 - 85.15: 6 Dihedral angle restraints: 5069 sinusoidal: 2129 harmonic: 2940 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N HIS A 572 " pdb=" CA HIS A 572 " ideal model delta harmonic sigma weight residual 180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP A 290 " pdb=" C TRP A 290 " pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1268 0.084 - 0.168: 74 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 7OK T 9 " pdb=" C3' 7OK T 9 " pdb=" O2' 7OK T 9 " pdb=" C1' 7OK T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.33 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ASN A 138 " pdb=" N ASN A 138 " pdb=" C ASN A 138 " pdb=" CB ASN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 7OK T 9 " -0.081 2.00e-02 2.50e+03 1.18e-01 3.48e+02 pdb=" N1 7OK T 9 " -0.008 2.00e-02 2.50e+03 pdb=" C2 7OK T 9 " -0.016 2.00e-02 2.50e+03 pdb=" O2 7OK T 9 " -0.068 2.00e-02 2.50e+03 pdb=" N3 7OK T 9 " 0.040 2.00e-02 2.50e+03 pdb=" C4 7OK T 9 " 0.099 2.00e-02 2.50e+03 pdb=" N4 7OK T 9 " 0.160 2.00e-02 2.50e+03 pdb=" C5 7OK T 9 " 0.105 2.00e-02 2.50e+03 pdb=" C6 7OK T 9 " 0.048 2.00e-02 2.50e+03 pdb=" OAC 7OK T 9 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.042 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 927 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C LEU A 758 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1177 2.75 - 3.29: 8132 3.29 - 3.83: 14217 3.83 - 4.36: 17446 4.36 - 4.90: 29370 Nonbonded interactions: 70342 Sorted by model distance: nonbonded pdb=" OD2 ASP A 260 " pdb=" OG1 THR A 262 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS A 426 " pdb=" OE1 GLN A 886 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 343 " pdb=" OD2 ASP A 377 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.234 2.440 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.241 2.440 ... (remaining 70337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.940 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.007 0.214 8642 Z= 0.427 Angle : 0.522 11.948 11831 Z= 0.284 Chirality : 0.041 0.420 1343 Planarity : 0.005 0.118 1425 Dihedral : 12.440 85.155 3171 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.39 (0.26), residues: 979 helix: 0.69 (0.25), residues: 459 sheet: -0.09 (0.52), residues: 96 loop : 0.02 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.935 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2342 time to fit residues: 37.1060 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8642 Z= 0.317 Angle : 0.524 6.310 11831 Z= 0.275 Chirality : 0.042 0.142 1343 Planarity : 0.004 0.043 1425 Dihedral : 5.940 51.697 1333 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.33 (0.26), residues: 979 helix: 0.68 (0.24), residues: 459 sheet: -0.13 (0.51), residues: 96 loop : -0.04 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.003 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 102 average time/residue: 0.1996 time to fit residues: 29.3563 Evaluate side-chains 96 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0851 time to fit residues: 2.0120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8642 Z= 0.223 Angle : 0.455 5.994 11831 Z= 0.240 Chirality : 0.039 0.144 1343 Planarity : 0.003 0.043 1425 Dihedral : 6.028 56.839 1333 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.55 (0.26), residues: 979 helix: 0.86 (0.24), residues: 460 sheet: 0.19 (0.56), residues: 85 loop : 0.02 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.879 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.2016 time to fit residues: 28.0246 Evaluate side-chains 99 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0806 time to fit residues: 2.4542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8642 Z= 0.267 Angle : 0.478 6.014 11831 Z= 0.252 Chirality : 0.040 0.144 1343 Planarity : 0.003 0.045 1425 Dihedral : 6.191 63.166 1333 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.50 (0.26), residues: 979 helix: 0.82 (0.24), residues: 460 sheet: 0.17 (0.56), residues: 85 loop : -0.03 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.952 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 104 average time/residue: 0.2148 time to fit residues: 32.0600 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0813 time to fit residues: 1.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 8642 Z= 0.437 Angle : 0.567 6.185 11831 Z= 0.300 Chirality : 0.044 0.151 1343 Planarity : 0.004 0.049 1425 Dihedral : 6.444 65.724 1333 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 979 helix: 0.51 (0.24), residues: 465 sheet: -0.43 (0.50), residues: 98 loop : -0.26 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.883 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 112 average time/residue: 0.2056 time to fit residues: 32.6470 Evaluate side-chains 105 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0811 time to fit residues: 2.3515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8642 Z= 0.243 Angle : 0.469 5.892 11831 Z= 0.247 Chirality : 0.040 0.139 1343 Planarity : 0.003 0.051 1425 Dihedral : 6.353 71.775 1333 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.29 (0.26), residues: 979 helix: 0.69 (0.24), residues: 465 sheet: 0.01 (0.56), residues: 85 loop : -0.17 (0.28), residues: 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.831 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.2047 time to fit residues: 30.8762 Evaluate side-chains 99 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0787 time to fit residues: 1.6508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8642 Z= 0.141 Angle : 0.425 6.317 11831 Z= 0.223 Chirality : 0.038 0.133 1343 Planarity : 0.003 0.049 1425 Dihedral : 6.271 77.798 1333 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 979 helix: 0.90 (0.24), residues: 470 sheet: 0.16 (0.57), residues: 85 loop : -0.04 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.956 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.2163 time to fit residues: 31.0456 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0818 time to fit residues: 1.7435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 8642 Z= 0.344 Angle : 0.524 6.058 11831 Z= 0.276 Chirality : 0.042 0.148 1343 Planarity : 0.004 0.050 1425 Dihedral : 6.403 77.457 1333 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.28 (0.26), residues: 979 helix: 0.73 (0.24), residues: 465 sheet: -0.32 (0.51), residues: 100 loop : -0.16 (0.29), residues: 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.926 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 0.2183 time to fit residues: 31.2100 Evaluate side-chains 102 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0884 time to fit residues: 1.8985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8642 Z= 0.148 Angle : 0.435 6.337 11831 Z= 0.228 Chirality : 0.038 0.136 1343 Planarity : 0.003 0.051 1425 Dihedral : 6.319 81.145 1333 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.50 (0.26), residues: 979 helix: 0.88 (0.24), residues: 470 sheet: 0.11 (0.57), residues: 85 loop : -0.11 (0.28), residues: 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.954 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2187 time to fit residues: 30.6995 Evaluate side-chains 98 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0827 time to fit residues: 1.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8642 Z= 0.143 Angle : 0.429 5.918 11831 Z= 0.224 Chirality : 0.038 0.135 1343 Planarity : 0.003 0.051 1425 Dihedral : 6.250 83.144 1333 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.61 (0.26), residues: 979 helix: 0.98 (0.24), residues: 470 sheet: 0.07 (0.57), residues: 85 loop : -0.05 (0.28), residues: 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.920 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2153 time to fit residues: 30.5049 Evaluate side-chains 98 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.1980 chunk 11 optimal weight: 0.0170 chunk 22 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.159759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137547 restraints weight = 9052.916| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.36 r_work: 0.3363 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8642 Z= 0.111 Angle : 0.413 6.319 11831 Z= 0.215 Chirality : 0.037 0.145 1343 Planarity : 0.003 0.050 1425 Dihedral : 6.211 85.178 1333 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 979 helix: 1.09 (0.25), residues: 475 sheet: 0.05 (0.56), residues: 85 loop : 0.04 (0.29), residues: 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1774.27 seconds wall clock time: 33 minutes 6.29 seconds (1986.29 seconds total)