Starting phenix.real_space_refine on Mon Mar 18 15:16:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/03_2024/7lyc_23592.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 29 5.16 5 C 8834 2.51 5 N 2874 2.21 5 O 3445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "N GLU 634": "OE1" <-> "OE2" Residue "N GLU 740": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 639 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "N" Number of atoms: 2683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 bond proxies already assigned to first conformer: 2702 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ASER N 452 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER N 452 " occ=0.50 Time building chain proxies: 8.04, per 1000 atoms: 0.52 Number of scatterers: 15475 At special positions: 0 Unit cell: (108.926, 117.146, 118.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 293 15.00 O 3445 8.00 N 2874 7.00 C 8834 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: 7.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 61.7% alpha, 5.8% beta 140 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.677A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.520A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.661A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.505A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'N' and resid 430 through 439 Processing helix chain 'N' and resid 440 through 450 Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 473 through 483 Processing helix chain 'N' and resid 491 through 495 Processing helix chain 'N' and resid 496 through 505 Processing helix chain 'N' and resid 506 through 516 Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 536 through 544 Processing helix chain 'N' and resid 578 through 593 Processing helix chain 'N' and resid 617 through 626 Processing helix chain 'N' and resid 633 through 643 removed outlier: 3.554A pdb=" N LYS N 637 " --> pdb=" O PHE N 633 " (cutoff:3.500A) Processing helix chain 'N' and resid 648 through 652 removed outlier: 3.804A pdb=" N GLU N 652 " --> pdb=" O GLU N 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 666 removed outlier: 3.915A pdb=" N SER N 660 " --> pdb=" O GLY N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 687 through 698 Processing helix chain 'N' and resid 711 through 716 Processing helix chain 'N' and resid 760 through 770 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.943A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.369A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.085A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.951A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.399A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.104A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 17 removed outlier: 9.097A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 595 through 597 removed outlier: 4.380A pdb=" N GLY N 574 " --> pdb=" O TYR N 597 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL N 571 " --> pdb=" O HIS N 606 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL N 608 " --> pdb=" O VAL N 571 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE N 573 " --> pdb=" O VAL N 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 701 through 702 removed outlier: 6.455A pdb=" N TYR N 676 " --> pdb=" O TYR N 736 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE N 738 " --> pdb=" O TYR N 676 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR N 678 " --> pdb=" O ILE N 738 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN N 735 " --> pdb=" O TRP N 756 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA N 758 " --> pdb=" O GLN N 735 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE N 737 " --> pdb=" O ALA N 758 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1559 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1965 1.32 - 1.44: 5712 1.44 - 1.56: 8057 1.56 - 1.69: 584 1.69 - 1.81: 45 Bond restraints: 16363 Sorted by residual: bond pdb=" C GLU E 50 " pdb=" O GLU E 50 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" C ARG E 116 " pdb=" O ARG E 116 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.28e-02 6.10e+03 9.86e+00 bond pdb=" C LYS D 116 " pdb=" O LYS D 116 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" C VAL E 117 " pdb=" O VAL E 117 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.19e-02 7.06e+03 7.95e+00 bond pdb=" C GLN A 76 " pdb=" N ASP A 77 " ideal model delta sigma weight residual 1.335 1.301 0.034 1.34e-02 5.57e+03 6.47e+00 ... (remaining 16358 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.58: 1490 105.58 - 112.68: 9082 112.68 - 119.78: 5371 119.78 - 126.88: 6595 126.88 - 133.98: 822 Bond angle restraints: 23360 Sorted by residual: angle pdb=" N ALA A 114 " pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 113.15 108.44 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" N GLU C 91 " pdb=" CA GLU C 91 " pdb=" C GLU C 91 " ideal model delta sigma weight residual 111.36 115.33 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.36 107.58 3.78 1.09e+00 8.42e-01 1.20e+01 angle pdb=" N ARG A 116 " pdb=" CA ARG A 116 " pdb=" C ARG A 116 " ideal model delta sigma weight residual 109.41 104.69 4.72 1.52e+00 4.33e-01 9.64e+00 angle pdb=" N GLU A 50 " pdb=" CA GLU A 50 " pdb=" C GLU A 50 " ideal model delta sigma weight residual 111.28 114.41 -3.13 1.09e+00 8.42e-01 8.24e+00 ... (remaining 23355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7528 33.16 - 66.31: 1551 66.31 - 99.47: 38 99.47 - 132.62: 0 132.62 - 165.78: 2 Dihedral angle restraints: 9119 sinusoidal: 5667 harmonic: 3452 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 54.22 165.78 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.57 153.43 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 9116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2311 0.062 - 0.123: 313 0.123 - 0.185: 20 0.185 - 0.247: 0 0.247 - 0.308: 1 Chirality restraints: 2645 Sorted by residual: chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LEU N 625 " pdb=" N LEU N 625 " pdb=" C LEU N 625 " pdb=" CB LEU N 625 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE N 573 " pdb=" N ILE N 573 " pdb=" C ILE N 573 " pdb=" CB ILE N 573 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2642 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " 0.011 2.00e-02 2.50e+03 1.36e-02 5.57e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " -0.033 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 103 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 496 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO N 497 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 497 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 497 " 0.028 5.00e-02 4.00e+02 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 3 2.03 - 2.75: 1847 2.75 - 3.47: 19710 3.47 - 4.18: 44026 4.18 - 4.90: 68237 Nonbonded interactions: 133823 Sorted by model distance: nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.314 3.350 nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.329 3.350 nonbonded pdb=" NH1 ARG N 427 " pdb=" OE1 GLU N 429 " model vdw 1.972 2.520 nonbonded pdb=" O ASN N 626 " pdb=" OD1 ASN N 626 " model vdw 2.086 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.179 2.496 ... (remaining 133818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = (chain 'F' and (resid 20 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 4.240 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 49.700 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.006 0.048 16363 Z= 0.349 Angle : 0.647 5.980 23360 Z= 0.396 Chirality : 0.042 0.308 2645 Planarity : 0.005 0.051 1948 Dihedral : 25.815 165.775 6895 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 0.69 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1172 helix: 0.47 (0.19), residues: 709 sheet: 0.08 (0.69), residues: 58 loop : -0.73 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 629 HIS 0.002 0.001 HIS C 31 PHE 0.010 0.002 PHE A 78 TYR 0.016 0.002 TYR H 121 ARG 0.013 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8406 (pp30) cc_final: 0.7784 (pt0) REVERT: A 129 ARG cc_start: 0.7873 (tpt-90) cc_final: 0.7258 (ttp-170) REVERT: B 74 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7442 (mt-10) REVERT: D 85 LYS cc_start: 0.9011 (mttp) cc_final: 0.8765 (mtmm) REVERT: D 99 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7965 (mtt180) REVERT: H 34 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7119 (mmtm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 2.0729 time to fit residues: 324.1868 Evaluate side-chains 111 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN B 75 HIS E 68 GLN E 76 GLN N 626 ASN C 104 GLN G 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.222 Angle : 0.563 6.473 23360 Z= 0.334 Chirality : 0.037 0.191 2645 Planarity : 0.005 0.046 1948 Dihedral : 28.865 166.851 4517 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.08 % Allowed : 7.58 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1172 helix: 1.41 (0.19), residues: 718 sheet: 0.13 (0.69), residues: 58 loop : -0.49 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 629 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.016 0.001 TYR D 121 ARG 0.006 0.000 ARG N 529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8354 (pp30) cc_final: 0.7786 (pt0) REVERT: A 129 ARG cc_start: 0.8171 (tpt-90) cc_final: 0.7452 (tmt170) REVERT: B 74 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7517 (mt-10) REVERT: D 71 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: D 86 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6682 (mtp85) REVERT: D 93 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: D 99 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.7993 (mtt180) REVERT: H 34 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7112 (mmtm) REVERT: H 99 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7986 (mtt180) REVERT: N 425 ASN cc_start: 0.8411 (p0) cc_final: 0.8153 (p0) REVERT: N 722 TYR cc_start: 0.8934 (t80) cc_final: 0.8689 (t80) outliers start: 10 outliers final: 5 residues processed: 127 average time/residue: 1.8970 time to fit residues: 258.0912 Evaluate side-chains 124 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 689 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 93 GLN N 470 ASN N 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16363 Z= 0.270 Angle : 0.571 6.834 23360 Z= 0.337 Chirality : 0.038 0.195 2645 Planarity : 0.005 0.047 1948 Dihedral : 28.932 166.578 4517 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.87 % Allowed : 9.15 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1172 helix: 1.58 (0.19), residues: 720 sheet: 0.20 (0.72), residues: 53 loop : -0.40 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 629 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE G 25 TYR 0.015 0.002 TYR D 121 ARG 0.006 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8417 (pp30) cc_final: 0.7723 (pt0) REVERT: A 129 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7463 (tmt170) REVERT: B 74 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 91 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8133 (tttp) REVERT: D 71 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: D 86 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6675 (mtp85) REVERT: D 93 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: D 99 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.8031 (mtt180) REVERT: H 34 LYS cc_start: 0.8014 (ptmt) cc_final: 0.7081 (mmtm) REVERT: N 425 ASN cc_start: 0.8442 (p0) cc_final: 0.8171 (p0) REVERT: N 649 GLU cc_start: 0.5044 (OUTLIER) cc_final: 0.4739 (mt-10) REVERT: N 722 TYR cc_start: 0.8933 (t80) cc_final: 0.8689 (t80) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 1.9055 time to fit residues: 256.8932 Evaluate side-chains 127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 689 ASP Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.218 Angle : 0.558 6.914 23360 Z= 0.331 Chirality : 0.037 0.213 2645 Planarity : 0.004 0.045 1948 Dihedral : 28.921 166.870 4517 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.77 % Allowed : 10.63 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1172 helix: 1.71 (0.19), residues: 720 sheet: 0.23 (0.73), residues: 53 loop : -0.37 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 756 HIS 0.007 0.001 HIS N 483 PHE 0.007 0.001 PHE E 67 TYR 0.013 0.001 TYR D 121 ARG 0.005 0.000 ARG N 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8309 (pp30) cc_final: 0.7563 (pt0) REVERT: B 74 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 91 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8113 (tttp) REVERT: D 71 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: D 85 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8044 (mtmm) REVERT: D 86 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6688 (mtp85) REVERT: D 93 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: D 99 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.8023 (mtt180) REVERT: H 34 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7109 (mmtm) REVERT: H 99 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7964 (mtt180) REVERT: N 425 ASN cc_start: 0.8392 (p0) cc_final: 0.8129 (p0) REVERT: N 649 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.4737 (mt-10) REVERT: N 722 TYR cc_start: 0.8930 (t80) cc_final: 0.8690 (t80) outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 1.8731 time to fit residues: 253.2021 Evaluate side-chains 131 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 689 ASP Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16363 Z= 0.275 Angle : 0.568 7.335 23360 Z= 0.335 Chirality : 0.038 0.209 2645 Planarity : 0.004 0.046 1948 Dihedral : 28.938 167.947 4517 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.97 % Allowed : 11.61 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1172 helix: 1.68 (0.19), residues: 720 sheet: 0.31 (0.74), residues: 53 loop : -0.38 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 629 HIS 0.004 0.001 HIS N 483 PHE 0.008 0.001 PHE A 78 TYR 0.015 0.002 TYR D 121 ARG 0.008 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8344 (pp30) cc_final: 0.7632 (pt0) REVERT: A 90 MET cc_start: 0.8184 (mmp) cc_final: 0.7978 (mmm) REVERT: B 74 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 91 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8132 (tttp) REVERT: D 71 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: D 85 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: D 86 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.6803 (mtp85) REVERT: D 93 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: D 99 ARG cc_start: 0.8288 (mtt-85) cc_final: 0.8000 (mtt180) REVERT: H 34 LYS cc_start: 0.8030 (ptmt) cc_final: 0.7110 (mmtm) REVERT: N 425 ASN cc_start: 0.8411 (p0) cc_final: 0.8130 (p0) REVERT: N 474 LEU cc_start: 0.7555 (mm) cc_final: 0.7112 (mp) REVERT: N 649 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4964 (mt-10) REVERT: N 722 TYR cc_start: 0.8944 (t80) cc_final: 0.8688 (t80) outliers start: 19 outliers final: 10 residues processed: 133 average time/residue: 1.8326 time to fit residues: 261.3233 Evaluate side-chains 133 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 689 ASP Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 113 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN N 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16363 Z= 0.174 Angle : 0.546 8.682 23360 Z= 0.325 Chirality : 0.036 0.192 2645 Planarity : 0.004 0.045 1948 Dihedral : 28.906 168.505 4517 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.26 % Allowed : 11.61 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1172 helix: 1.90 (0.19), residues: 720 sheet: 0.33 (0.75), residues: 53 loop : -0.30 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 629 HIS 0.003 0.001 HIS N 483 PHE 0.007 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.006 0.000 ARG N 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8226 (pp30) cc_final: 0.7507 (pt0) REVERT: A 90 MET cc_start: 0.8171 (mmp) cc_final: 0.7954 (mmm) REVERT: B 74 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 91 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8079 (tttp) REVERT: D 71 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: D 85 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: D 86 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.6679 (mtp85) REVERT: D 93 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: D 99 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7985 (mtt180) REVERT: H 34 LYS cc_start: 0.8026 (ptmt) cc_final: 0.7093 (mmtm) REVERT: N 425 ASN cc_start: 0.8349 (p0) cc_final: 0.7946 (p0) REVERT: N 474 LEU cc_start: 0.7547 (mm) cc_final: 0.7108 (mp) REVERT: N 584 MET cc_start: 0.3828 (OUTLIER) cc_final: 0.3424 (ppp) REVERT: N 722 TYR cc_start: 0.8938 (t80) cc_final: 0.8663 (t80) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 1.8135 time to fit residues: 245.5143 Evaluate side-chains 130 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 584 MET Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 689 ASP Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 16363 Z= 0.551 Angle : 0.695 8.339 23360 Z= 0.397 Chirality : 0.048 0.221 2645 Planarity : 0.006 0.055 1948 Dihedral : 29.305 166.973 4517 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.26 % Allowed : 13.09 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1172 helix: 1.27 (0.19), residues: 719 sheet: 0.20 (0.73), residues: 53 loop : -0.65 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 462 HIS 0.004 0.001 HIS N 483 PHE 0.019 0.003 PHE A 78 TYR 0.021 0.002 TYR D 121 ARG 0.007 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8048 (tttm) REVERT: A 76 GLN cc_start: 0.8548 (pp30) cc_final: 0.8044 (pt0) REVERT: B 74 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 91 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8164 (tttp) REVERT: D 71 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: D 85 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8042 (mtmm) REVERT: D 99 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.7951 (mtt180) REVERT: H 34 LYS cc_start: 0.8064 (ptmt) cc_final: 0.7090 (mmtm) REVERT: N 664 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6440 (tpt-90) REVERT: G 92 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8112 (mt-10) outliers start: 22 outliers final: 11 residues processed: 127 average time/residue: 1.8527 time to fit residues: 253.6492 Evaluate side-chains 130 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 690 ASN Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16363 Z= 0.258 Angle : 0.584 8.681 23360 Z= 0.344 Chirality : 0.039 0.186 2645 Planarity : 0.004 0.046 1948 Dihedral : 29.184 171.206 4517 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.77 % Allowed : 13.78 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1172 helix: 1.56 (0.19), residues: 720 sheet: 0.28 (0.75), residues: 53 loop : -0.47 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 756 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 78 TYR 0.014 0.002 TYR D 121 ARG 0.005 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.353 Fit side-chains REVERT: A 76 GLN cc_start: 0.8409 (pp30) cc_final: 0.7846 (pt0) REVERT: A 90 MET cc_start: 0.8154 (mmp) cc_final: 0.7849 (mmm) REVERT: B 74 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 91 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8119 (tttp) REVERT: D 71 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: D 85 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8070 (mtmm) REVERT: D 86 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6830 (mtp85) REVERT: D 93 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: D 99 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7981 (mtt180) REVERT: H 34 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7164 (mmtm) REVERT: N 474 LEU cc_start: 0.7547 (mm) cc_final: 0.7045 (mp) REVERT: N 664 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6430 (tpt-90) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 1.8542 time to fit residues: 248.7745 Evaluate side-chains 131 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 690 ASN Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16363 Z= 0.184 Angle : 0.555 8.471 23360 Z= 0.330 Chirality : 0.037 0.186 2645 Planarity : 0.004 0.042 1948 Dihedral : 29.021 171.776 4517 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 14.17 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1172 helix: 1.81 (0.19), residues: 720 sheet: 0.38 (0.76), residues: 53 loop : -0.35 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR N 676 ARG 0.009 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8187 (pp30) cc_final: 0.7505 (pt0) REVERT: A 90 MET cc_start: 0.8200 (mmp) cc_final: 0.7933 (mmm) REVERT: B 74 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 91 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8102 (tttp) REVERT: D 71 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: D 85 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8006 (mtmm) REVERT: D 86 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.6796 (mtp85) REVERT: D 93 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: D 99 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7985 (mtt180) REVERT: H 34 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7159 (mmtm) REVERT: N 474 LEU cc_start: 0.7537 (mm) cc_final: 0.7048 (mp) REVERT: N 722 TYR cc_start: 0.8976 (t80) cc_final: 0.8724 (t80) outliers start: 14 outliers final: 8 residues processed: 122 average time/residue: 1.8484 time to fit residues: 241.7645 Evaluate side-chains 127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 690 ASN Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN N 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16363 Z= 0.239 Angle : 0.559 9.582 23360 Z= 0.330 Chirality : 0.037 0.168 2645 Planarity : 0.004 0.044 1948 Dihedral : 28.917 172.203 4517 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.48 % Allowed : 14.47 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1172 helix: 1.85 (0.19), residues: 720 sheet: 0.36 (0.76), residues: 53 loop : -0.31 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 462 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.013 0.001 TYR D 121 ARG 0.009 0.000 ARG C 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8222 (pp30) cc_final: 0.7563 (pt0) REVERT: A 90 MET cc_start: 0.8185 (mmp) cc_final: 0.7967 (mmm) REVERT: B 74 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 91 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8111 (tttp) REVERT: D 71 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: D 85 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7963 (mtmm) REVERT: D 93 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: D 99 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8005 (mtt180) REVERT: H 34 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7173 (mmtm) REVERT: N 425 ASN cc_start: 0.8381 (p0) cc_final: 0.7969 (p0) REVERT: N 474 LEU cc_start: 0.7540 (mm) cc_final: 0.7041 (mp) REVERT: N 722 TYR cc_start: 0.8953 (t80) cc_final: 0.8681 (t80) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 1.8324 time to fit residues: 240.1564 Evaluate side-chains 127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 664 ARG Chi-restraints excluded: chain N residue 690 ASN Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 76 GLN N 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.198062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156159 restraints weight = 30019.779| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.86 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16363 Z= 0.178 Angle : 0.549 9.058 23360 Z= 0.326 Chirality : 0.036 0.160 2645 Planarity : 0.004 0.047 1948 Dihedral : 28.912 172.206 4517 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 14.67 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1172 helix: 1.94 (0.19), residues: 718 sheet: 0.37 (0.76), residues: 53 loop : -0.31 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 629 HIS 0.003 0.001 HIS N 483 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.001 TYR N 676 ARG 0.008 0.000 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.64 seconds wall clock time: 79 minutes 8.94 seconds (4748.94 seconds total)