Starting phenix.real_space_refine on Sun Jul 21 04:07:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/07_2024/8pc6_17595.cif" } resolution = 3.04 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 15 5.16 5 C 7600 2.51 5 N 2518 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13493 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "'] Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3014 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 9.63, per 1000 atoms: 0.71 Number of scatterers: 13493 At special positions: 0 Unit cell: (104.2, 140.045, 120.872, 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 15 16.00 P 293 15.00 O 3067 8.00 N 2518 7.00 C 7600 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: 7.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 59.5% alpha, 6.2% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.602A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.583A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.882A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.826A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.556A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.501A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.899A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.251A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.666A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.546A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.234A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'L' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.649A 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: 6.464A 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 'C' and resid 42 through 43 removed outlier: 7.155A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.424A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.950A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.967A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2773 1.33 - 1.45: 4380 1.45 - 1.57: 6591 1.57 - 1.69: 584 1.69 - 1.81: 30 Bond restraints: 14358 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" N LEU L 53 " pdb=" CA LEU L 53 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 4.99e+00 bond pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" C3' DT J -72 " pdb=" O3' DT J -72 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.44e+00 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.62: 1194 104.62 - 111.97: 7773 111.97 - 119.31: 4573 119.31 - 126.65: 6149 126.65 - 133.99: 933 Bond angle restraints: 20622 Sorted by residual: angle pdb=" CB MET L 1 " pdb=" CG MET L 1 " pdb=" SD MET L 1 " ideal model delta sigma weight residual 112.70 125.42 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " pdb=" P DA I 50 " ideal model delta sigma weight residual 120.20 125.88 -5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" CB LEU L 53 " ideal model delta sigma weight residual 111.55 105.15 6.40 1.74e+00 3.30e-01 1.35e+01 angle pdb=" CA TYR L 61 " pdb=" CB TYR L 61 " pdb=" CG TYR L 61 " ideal model delta sigma weight residual 113.90 120.41 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N MET L 1 " pdb=" CA MET L 1 " pdb=" C MET L 1 " ideal model delta sigma weight residual 111.00 101.39 9.61 2.80e+00 1.28e-01 1.18e+01 ... (remaining 20617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 6328 35.96 - 71.91: 1552 71.91 - 107.86: 27 107.86 - 143.82: 3 143.82 - 179.77: 3 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 40.23 179.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.50 -165.50 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.32 -158.32 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2023 0.064 - 0.127: 278 0.127 - 0.191: 14 0.191 - 0.254: 5 0.254 - 0.318: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA LEU L 53 " pdb=" N LEU L 53 " pdb=" C LEU L 53 " pdb=" CB LEU L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE L 58 " pdb=" CA ILE L 58 " pdb=" CG1 ILE L 58 " pdb=" CG2 ILE L 58 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1' DT J -72 " pdb=" O4' DT J -72 " pdb=" C2' DT J -72 " pdb=" N1 DT J -72 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C LYS F 59 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LEU F 62 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 108 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL D 108 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL D 108 " -0.021 2.00e-02 2.50e+03 pdb=" N SER D 109 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 454 2.69 - 3.25: 11465 3.25 - 3.80: 25026 3.80 - 4.35: 31928 4.35 - 4.90: 46216 Nonbonded interactions: 115089 Sorted by model distance: nonbonded pdb=" O TYR L 61 " pdb=" NZ LYS L 65 " model vdw 2.142 2.520 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.206 2.440 nonbonded pdb=" N THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.215 2.520 nonbonded pdb=" NH1 ARG A 129 " pdb=" OD1 ASP E 106 " model vdw 2.286 2.520 nonbonded pdb=" N4 DC I 51 " pdb=" O6 DG J -51 " model vdw 2.310 2.520 ... (remaining 115084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 46.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14358 Z= 0.205 Angle : 0.682 12.723 20622 Z= 0.402 Chirality : 0.044 0.318 2322 Planarity : 0.007 0.074 1605 Dihedral : 28.540 179.771 6157 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % 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 (0.27), residues: 913 helix: 1.72 (0.22), residues: 556 sheet: -3.79 (0.60), residues: 23 loop : -1.15 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 21 HIS 0.004 0.001 HIS K 20 PHE 0.041 0.002 PHE C 25 TYR 0.030 0.001 TYR L 61 ARG 0.018 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.134 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.3790 time to fit residues: 88.8060 Evaluate side-chains 111 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 93 GLN K 20 HIS K 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14358 Z= 0.241 Angle : 0.573 8.167 20622 Z= 0.337 Chirality : 0.037 0.176 2322 Planarity : 0.005 0.046 1605 Dihedral : 30.973 163.446 4252 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.14 % Allowed : 7.73 % Favored : 91.13 % 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: 1.64 (0.28), residues: 913 helix: 2.34 (0.22), residues: 568 sheet: -3.43 (0.68), residues: 23 loop : -0.91 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 21 HIS 0.004 0.001 HIS D 46 PHE 0.020 0.002 PHE C 25 TYR 0.010 0.001 TYR G 50 ARG 0.011 0.000 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.165 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3054 (tmm) cc_final: 0.2117 (tpp) REVERT: L 53 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4312 (mp) outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.3314 time to fit residues: 54.3219 Evaluate side-chains 108 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 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 C 73 ASN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14358 Z= 0.200 Angle : 0.523 7.357 20622 Z= 0.310 Chirality : 0.035 0.154 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.506 160.378 4252 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 8.49 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.28), residues: 913 helix: 2.61 (0.22), residues: 575 sheet: -3.37 (0.75), residues: 23 loop : -0.97 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.014 0.001 PHE C 25 TYR 0.015 0.001 TYR L 61 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.194 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3264 (tmm) cc_final: 0.2775 (tpt) outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 0.3137 time to fit residues: 50.2557 Evaluate side-chains 101 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 77 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14358 Z= 0.233 Angle : 0.534 6.636 20622 Z= 0.314 Chirality : 0.035 0.138 2322 Planarity : 0.004 0.047 1605 Dihedral : 30.447 179.368 4250 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.27 % Allowed : 10.01 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.28), residues: 913 helix: 2.71 (0.22), residues: 575 sheet: -2.57 (0.68), residues: 36 loop : -0.80 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 21 HIS 0.003 0.001 HIS C 31 PHE 0.019 0.001 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.081 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: L 1 MET cc_start: 0.3319 (tmm) cc_final: 0.2966 (tpp) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 0.3236 time to fit residues: 47.7033 Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 77 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14358 Z= 0.315 Angle : 0.573 8.781 20622 Z= 0.335 Chirality : 0.038 0.165 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.501 175.706 4250 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 11.03 % Favored : 88.09 % 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: 1.90 (0.28), residues: 913 helix: 2.57 (0.22), residues: 575 sheet: -2.98 (0.66), residues: 37 loop : -0.84 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 21 HIS 0.003 0.001 HIS D 79 PHE 0.024 0.002 PHE C 25 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG L 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.198 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7999 (mptp) REVERT: L 1 MET cc_start: 0.3815 (tmm) cc_final: 0.3601 (tpp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.3427 time to fit residues: 49.2631 Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14358 Z= 0.170 Angle : 0.515 9.938 20622 Z= 0.303 Chirality : 0.034 0.149 2322 Planarity : 0.004 0.043 1605 Dihedral : 30.117 175.692 4250 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.89 % Allowed : 11.41 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.28), residues: 913 helix: 2.89 (0.22), residues: 575 sheet: -2.95 (0.62), residues: 37 loop : -0.70 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.013 0.001 PHE K 77 TYR 0.009 0.001 TYR F 51 ARG 0.006 0.000 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.115 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7995 (mptp) outliers start: 7 outliers final: 3 residues processed: 103 average time/residue: 0.3321 time to fit residues: 46.6085 Evaluate side-chains 93 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 78 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14358 Z= 0.251 Angle : 0.542 9.730 20622 Z= 0.317 Chirality : 0.036 0.150 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.245 179.964 4250 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.76 % Allowed : 12.29 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.28), residues: 913 helix: 2.78 (0.22), residues: 575 sheet: -3.14 (0.57), residues: 36 loop : -0.66 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.002 PHE C 25 TYR 0.016 0.001 TYR L 61 ARG 0.004 0.000 ARG L 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.166 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7999 (mptp) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.3487 time to fit residues: 45.5115 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14358 Z= 0.226 Angle : 0.531 11.221 20622 Z= 0.311 Chirality : 0.035 0.138 2322 Planarity : 0.004 0.043 1605 Dihedral : 30.144 178.324 4250 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.76 % Allowed : 12.42 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.28), residues: 913 helix: 2.78 (0.22), residues: 575 sheet: -3.16 (0.59), residues: 36 loop : -0.66 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE K 77 TYR 0.009 0.001 TYR B 51 ARG 0.003 0.000 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.066 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7987 (mptp) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.3416 time to fit residues: 46.5917 Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14358 Z= 0.369 Angle : 0.597 11.026 20622 Z= 0.346 Chirality : 0.039 0.147 2322 Planarity : 0.005 0.043 1605 Dihedral : 30.507 172.562 4250 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.89 % Allowed : 12.80 % Favored : 86.31 % 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: 1.73 (0.28), residues: 913 helix: 2.45 (0.22), residues: 574 sheet: -3.55 (0.54), residues: 38 loop : -0.83 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP K 21 HIS 0.004 0.001 HIS C 31 PHE 0.030 0.002 PHE K 77 TYR 0.016 0.001 TYR L 61 ARG 0.007 0.001 ARG L 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.096 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7969 (mptp) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.3234 time to fit residues: 43.3745 Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14358 Z= 0.181 Angle : 0.532 13.680 20622 Z= 0.312 Chirality : 0.034 0.158 2322 Planarity : 0.004 0.058 1605 Dihedral : 30.190 177.423 4250 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.63 % Allowed : 13.43 % 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: 2.09 (0.28), residues: 913 helix: 2.76 (0.22), residues: 576 sheet: -3.46 (0.53), residues: 38 loop : -0.76 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 21 HIS 0.003 0.001 HIS K 48 PHE 0.014 0.001 PHE L 52 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.121 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (mptp) REVERT: L 56 LYS cc_start: 0.5626 (mmtt) cc_final: 0.5230 (tptm) REVERT: L 75 LYS cc_start: 0.7169 (tmmt) cc_final: 0.6912 (tmmt) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.3409 time to fit residues: 48.9773 Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 0.0060 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.080510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053079 restraints weight = 41497.268| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.83 r_work: 0.2776 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14358 Z= 0.176 Angle : 0.531 13.353 20622 Z= 0.309 Chirality : 0.034 0.155 2322 Planarity : 0.004 0.057 1605 Dihedral : 30.148 177.335 4250 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.38 % Allowed : 13.94 % Favored : 85.68 % 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: 2.20 (0.28), residues: 913 helix: 2.85 (0.22), residues: 576 sheet: -3.25 (0.49), residues: 50 loop : -0.61 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 21 HIS 0.003 0.001 HIS K 48 PHE 0.013 0.001 PHE L 43 TYR 0.021 0.001 TYR L 61 ARG 0.003 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.13 seconds wall clock time: 50 minutes 47.73 seconds (3047.73 seconds total)