Starting phenix.real_space_refine on Tue Nov 19 18:02:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/11_2024/7lyc_23592.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/11_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_23592/11_2024/7lyc_23592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/11_2024/7lyc_23592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/11_2024/7lyc_23592.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/11_2024/7lyc_23592.cif" } 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. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.02, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 3.65 Conformation dependent library (CDL) restraints added in 1.5 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: 7.39 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: 8.40 Time building geometry restraints manager: 4.20 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: 0.00 - 1.20: 21764 1.20 - 2.39: 1390 2.39 - 3.59: 171 3.59 - 4.78: 24 4.78 - 5.98: 11 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 3.120 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 Time spend for trying shortcut: 0.00 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.590 Find NCS groups from input model: 0.340 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.220 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.437 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: 2.1866 time to fit residues: 342.2777 Evaluate side-chains 111 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 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 55 GLN B 75 HIS E 68 GLN E 76 GLN F 93 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: 0.7885 moved from start: 0.0908 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= 0.286 Angle : 0.595 6.673 23360 Z= 0.350 Chirality : 0.039 0.194 2645 Planarity : 0.005 0.046 1948 Dihedral : 29.063 166.094 4517 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.08 % Allowed : 7.38 % Favored : 91.54 % 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: 718 sheet: 0.06 (0.71), residues: 53 loop : -0.60 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 629 HIS 0.004 0.001 HIS N 433 PHE 0.006 0.001 PHE G 25 TYR 0.015 0.002 TYR D 121 ARG 0.006 0.001 ARG E 49 *********************** 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 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8456 (pp30) cc_final: 0.7925 (pt0) REVERT: B 74 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 91 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8117 (tttp) REVERT: D 71 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: D 86 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.6700 (mtp85) REVERT: D 93 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: D 99 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.7996 (mtt180) REVERT: F 59 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7652 (mtmt) REVERT: H 34 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7175 (mmtm) outliers start: 10 outliers final: 4 residues processed: 125 average time/residue: 1.9872 time to fit residues: 265.9470 Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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: 3.9990 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16363 Z= 0.331 Angle : 0.600 6.707 23360 Z= 0.352 Chirality : 0.040 0.207 2645 Planarity : 0.005 0.048 1948 Dihedral : 29.075 165.895 4517 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.57 % Allowed : 9.74 % Favored : 88.68 % 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: 1.00 (0.24), residues: 1172 helix: 1.42 (0.19), residues: 718 sheet: -0.04 (0.71), residues: 53 loop : -0.54 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 629 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE E 78 TYR 0.015 0.002 TYR D 121 ARG 0.007 0.001 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 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8492 (pp30) cc_final: 0.7812 (pt0) REVERT: A 90 MET cc_start: 0.8237 (mmp) cc_final: 0.8034 (mmm) REVERT: B 74 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 91 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8099 (tttp) REVERT: D 71 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: D 86 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.6710 (mtp85) REVERT: D 99 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7992 (mtt180) REVERT: H 34 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7115 (mmtm) REVERT: N 649 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4843 (mt-10) REVERT: N 722 TYR cc_start: 0.8950 (t80) cc_final: 0.8710 (t80) outliers start: 15 outliers final: 5 residues processed: 122 average time/residue: 1.9717 time to fit residues: 257.2046 Evaluate side-chains 122 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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: 0.6980 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16363 Z= 0.183 Angle : 0.556 7.025 23360 Z= 0.332 Chirality : 0.037 0.158 2645 Planarity : 0.004 0.044 1948 Dihedral : 29.008 167.464 4517 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 11.52 % Favored : 87.30 % 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: 1.35 (0.24), residues: 1172 helix: 1.71 (0.19), residues: 719 sheet: -0.05 (0.72), residues: 53 loop : -0.42 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 629 HIS 0.009 0.001 HIS N 483 PHE 0.006 0.001 PHE A 67 TYR 0.012 0.001 TYR N 446 ARG 0.006 0.000 ARG C 71 *********************** 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 126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8251 (pp30) cc_final: 0.7515 (pt0) REVERT: A 90 MET cc_start: 0.8217 (mmp) cc_final: 0.8005 (mmm) REVERT: B 74 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7632 (mt-10) REVERT: D 71 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: D 85 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8083 (mtmm) REVERT: D 86 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.6725 (mtp85) REVERT: D 93 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: D 99 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7980 (mtt180) REVERT: F 59 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7536 (mtmt) REVERT: H 34 LYS cc_start: 0.8078 (ptmt) cc_final: 0.7140 (mmtm) REVERT: H 99 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7874 (mtt180) REVERT: N 649 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4830 (mt-10) REVERT: N 722 TYR cc_start: 0.8935 (t80) cc_final: 0.8674 (t80) outliers start: 11 outliers final: 3 residues processed: 119 average time/residue: 2.0535 time to fit residues: 261.1210 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 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: 4.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 0.0770 chunk 94 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16363 Z= 0.359 Angle : 0.607 6.909 23360 Z= 0.354 Chirality : 0.041 0.199 2645 Planarity : 0.005 0.049 1948 Dihedral : 29.096 166.311 4517 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.48 % Allowed : 12.60 % Favored : 85.93 % 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: 1.13 (0.24), residues: 1172 helix: 1.53 (0.19), residues: 720 sheet: 0.00 (0.72), residues: 53 loop : -0.51 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 629 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.002 PHE A 78 TYR 0.015 0.002 TYR D 121 ARG 0.007 0.001 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 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8476 (pp30) cc_final: 0.7849 (pt0) REVERT: A 90 MET cc_start: 0.8227 (mmp) cc_final: 0.8005 (mmm) REVERT: B 74 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7614 (mt-10) REVERT: B 91 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8083 (tttp) REVERT: D 71 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: D 85 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8051 (mtmm) REVERT: D 99 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7986 (mtt180) REVERT: H 34 LYS cc_start: 0.8094 (ptmt) cc_final: 0.7118 (mmtm) REVERT: N 474 LEU cc_start: 0.7621 (mm) cc_final: 0.7155 (mp) REVERT: N 649 GLU cc_start: 0.5045 (OUTLIER) cc_final: 0.4756 (mt-10) outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 2.0024 time to fit residues: 263.6582 Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 649 GLU 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 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16363 Z= 0.196 Angle : 0.563 7.849 23360 Z= 0.335 Chirality : 0.037 0.158 2645 Planarity : 0.004 0.045 1948 Dihedral : 29.044 167.922 4517 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 13.78 % Favored : 84.74 % 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: 1.41 (0.24), residues: 1172 helix: 1.77 (0.19), residues: 720 sheet: 0.04 (0.73), residues: 53 loop : -0.43 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.012 0.001 TYR N 676 ARG 0.007 0.000 ARG C 71 *********************** 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 130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.304 Fit side-chains REVERT: A 76 GLN cc_start: 0.8304 (pp30) cc_final: 0.7700 (pt0) REVERT: A 90 MET cc_start: 0.8207 (mmp) cc_final: 0.7990 (mmm) REVERT: B 74 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 91 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8072 (tttp) REVERT: D 71 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 85 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8004 (mtmm) REVERT: D 86 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6851 (mtp85) REVERT: D 93 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: D 99 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7973 (mtt180) REVERT: H 34 LYS cc_start: 0.8112 (ptmt) cc_final: 0.7127 (mmtm) REVERT: N 474 LEU cc_start: 0.7564 (mm) cc_final: 0.7099 (mp) REVERT: N 649 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4820 (mt-10) outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 1.6202 time to fit residues: 211.9246 Evaluate side-chains 122 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 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: 5.9990 chunk 114 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: