Starting phenix.real_space_refine on Sat Mar 16 02:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/03_2024/8pc6_17595_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/03_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_17595/03_2024/8pc6_17595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/03_2024/8pc6_17595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/03_2024/8pc6_17595_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc6_17595/03_2024/8pc6_17595_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.49, per 1000 atoms: 0.56 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: 6.89 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 37 helices and 2 sheets defined 52.6% alpha, 3.6% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.864A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 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 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.408A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 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 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.116A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP F 68 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 71 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.575A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'L' and resid 77 through 82 Processing sheet with id= A, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.688A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 58 through 60 removed outlier: 3.647A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 963 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: 4.65 Time building geometry restraints manager: 7.26 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: 458 2.69 - 3.25: 11500 3.25 - 3.80: 25064 3.80 - 4.35: 32068 4.35 - 4.90: 46251 Nonbonded interactions: 115341 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 115336 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: 0.010 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.940 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 43.810 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.360 ------------------------------------------------------------------------------- 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= 0.204 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 : 1.147 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: 0.4245 time to fit residues: 98.9354 Evaluate side-chains 111 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** ** C 84 GLN ** 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: 0.8110 moved from start: 0.2056 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= 0.234 Angle : 0.563 8.091 20622 Z= 0.333 Chirality : 0.037 0.155 2322 Planarity : 0.005 0.047 1605 Dihedral : 30.989 163.281 4252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.89 % Allowed : 7.60 % Favored : 91.51 % 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: 1.23 (0.27), residues: 913 helix: 1.99 (0.22), residues: 558 sheet: -3.41 (0.68), residues: 23 loop : -0.92 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 21 HIS 0.004 0.001 HIS D 46 PHE 0.020 0.001 PHE C 25 TYR 0.010 0.001 TYR G 50 ARG 0.008 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: 7 poor density : 113 time to evaluate : 1.052 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: 0.3172 (tmm) cc_final: 0.2267 (tpp) REVERT: L 53 LEU cc_start: 0.4521 (OUTLIER) cc_final: 0.4298 (mp) outliers start: 7 outliers final: 2 residues processed: 118 average time/residue: 0.3249 time to fit residues: 52.0203 Evaluate side-chains 108 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 L 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2691 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= 0.208 Angle : 0.527 6.903 20622 Z= 0.313 Chirality : 0.035 0.156 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.509 160.489 4252 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.14 % Allowed : 8.11 % Favored : 90.75 % 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: 1.33 (0.28), residues: 913 helix: 2.06 (0.22), residues: 561 sheet: -3.28 (0.73), residues: 23 loop : -0.91 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.001 PHE C 25 TYR 0.016 0.001 TYR L 61 ARG 0.003 0.000 ARG L 3 *********************** 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 117 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.230 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: 0.3134 (tmm) cc_final: 0.2600 (tpp) outliers start: 9 outliers final: 3 residues processed: 116 average time/residue: 0.3319 time to fit residues: 52.0625 Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14358 Z= 0.322 Angle : 0.573 7.224 20622 Z= 0.335 Chirality : 0.038 0.151 2322 Planarity : 0.005 0.041 1605 Dihedral : 30.652 178.621 4250 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 10.01 % Favored : 89.10 % 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: 1.14 (0.28), residues: 913 helix: 1.88 (0.22), residues: 562 sheet: -2.92 (0.65), residues: 37 loop : -0.83 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP K 21 HIS 0.003 0.001 HIS C 31 PHE 0.027 0.002 PHE C 25 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG L 3 *********************** 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 108 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.145 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: 0.8262 (OUTLIER) cc_final: 0.8007 (mptp) REVERT: D 30 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7463 (ttm170) outliers start: 7 outliers final: 5 residues processed: 106 average time/residue: 0.3455 time to fit residues: 49.2310 Evaluate side-chains 101 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 85 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14358 Z= 0.182 Angle : 0.514 8.743 20622 Z= 0.305 Chirality : 0.034 0.158 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.256 174.767 4250 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.01 % Allowed : 10.65 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 913 helix: 2.09 (0.22), residues: 564 sheet: -2.80 (0.64), residues: 38 loop : -0.66 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE C 25 TYR 0.009 0.001 TYR B 51 ARG 0.010 0.000 ARG L 74 *********************** 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 111 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.036 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: 0.8206 (OUTLIER) cc_final: 0.7957 (mptp) REVERT: C 56 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: D 30 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7395 (ttm170) REVERT: L 43 PHE cc_start: 0.4882 (m-10) cc_final: 0.4532 (m-10) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.3315 time to fit residues: 48.8905 Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 68 TYR 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: 2.9990 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.3533 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= 0.243 Angle : 0.536 9.305 20622 Z= 0.315 Chirality : 0.035 0.153 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.304 177.982 4250 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.63 % Allowed : 11.41 % Favored : 87.96 % 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 (0.28), residues: 913 helix: 2.04 (0.22), residues: 564 sheet: -2.73 (0.64), residues: 37 loop : -0.64 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.001 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.004 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 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.197 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: 0.8223 (OUTLIER) cc_final: 0.7981 (mptp) REVERT: C 56 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: D 30 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7418 (ttm170) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.3601 time to fit residues: 48.7173 Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 85 ASP 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: 0.9980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8186 moved from start: 0.3684 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= 0.236 Angle : 0.533 10.225 20622 Z= 0.312 Chirality : 0.035 0.146 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.200 179.465 4250 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.51 % Allowed : 12.42 % Favored : 87.07 % 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 (0.28), residues: 913 helix: 2.07 (0.22), residues: 564 sheet: -3.01 (0.57), residues: 38 loop : -0.65 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.003 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 99 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.206 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: 0.8232 (OUTLIER) cc_final: 0.7995 (mptp) REVERT: D 30 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7368 (ttm170) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.3622 time to fit residues: 47.6455 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER 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: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14358 Z= 0.317 Angle : 0.572 10.249 20622 Z= 0.332 Chirality : 0.037 0.144 2322 Planarity : 0.004 0.045 1605 Dihedral : 30.384 174.637 4250 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.63 % Allowed : 12.67 % Favored : 86.69 % 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: 1.22 (0.28), residues: 913 helix: 1.90 (0.22), residues: 563 sheet: -3.07 (0.54), residues: 37 loop : -0.70 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.018 0.002 PHE C 25 TYR 0.012 0.001 TYR B 51 ARG 0.006 0.001 ARG L 3 *********************** 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 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.131 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: 0.8234 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: D 30 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7445 (ttm170) outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.3373 time to fit residues: 42.3829 Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 86 ASN 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: 0.4980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14358 Z= 0.271 Angle : 0.563 12.651 20622 Z= 0.327 Chirality : 0.036 0.142 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.352 175.119 4250 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.63 % Allowed : 12.80 % Favored : 86.57 % 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: 1.22 (0.28), residues: 913 helix: 1.92 (0.22), residues: 563 sheet: -3.29 (0.50), residues: 38 loop : -0.69 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 21 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE L 52 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG L 24 *********************** 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 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.085 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: 0.8240 (OUTLIER) cc_final: 0.7975 (mptp) REVERT: D 30 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7446 (ttm170) outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.3512 time to fit residues: 44.2591 Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 12 PHE 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: 0.7980 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14358 Z= 0.192 Angle : 0.556 15.329 20622 Z= 0.321 Chirality : 0.035 0.139 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.348 175.677 4250 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.76 % Allowed : 12.55 % Favored : 86.69 % 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: 1.29 (0.28), residues: 913 helix: 2.00 (0.23), residues: 561 sheet: -3.28 (0.50), residues: 38 loop : -0.69 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 21 HIS 0.004 0.001 HIS K 48 PHE 0.013 0.001 PHE L 43 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG L 24 ********************** 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 106 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.147 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: 0.8233 (OUTLIER) cc_final: 0.7959 (mptp) REVERT: D 30 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7377 (ttm170) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 0.3364 time to fit residues: 46.6216 Evaluate side-chains 101 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 86 ASN 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: 0.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.0040 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.079342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051633 restraints weight = 41725.946| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.84 r_work: 0.2734 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14358 Z= 0.198 Angle : 0.553 14.948 20622 Z= 0.319 Chirality : 0.035 0.180 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.264 176.362 4250 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.63 % Allowed : 12.55 % 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: 1.37 (0.28), residues: 913 helix: 2.06 (0.23), residues: 561 sheet: -3.29 (0.50), residues: 38 loop : -0.66 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 21 HIS 0.002 0.001 HIS B 75 PHE 0.014 0.001 PHE K 45 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.15 seconds wall clock time: 50 minutes 8.70 seconds (3008.70 seconds total)