Starting phenix.real_space_refine on Sat Mar 16 06:30:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/03_2024/7yi1_33848_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 302 5.49 5 S 21 5.16 5 C 7843 2.51 5 N 2576 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "E ASP 77": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13926 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "K" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.43, per 1000 atoms: 0.53 Number of scatterers: 13926 At special positions: 0 Unit cell: (139.643, 141.808, 106.085, 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 21 16.00 P 302 15.00 O 3184 8.00 N 2576 7.00 C 7843 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: 6.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 55.4% alpha, 5.8% beta 146 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... 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 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.945A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 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 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' 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 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 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.838A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (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 37 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 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 101 through 120 Processing helix chain 'K' and resid 69 through 72 No H-bonds generated for 'chain 'K' and resid 69 through 72' Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 102 through 123 Processing helix chain 'L' and resid 102 through 123 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.057A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.537A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.134A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.521A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing sheet with id= A, first strand: chain 'K' and resid 13 through 18 removed outlier: 6.507A pdb=" N PHE K 78 " --> pdb=" O LEU K 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 29 through 32 Processing sheet with id= C, first strand: chain 'L' and resid 13 through 18 removed outlier: 3.621A pdb=" N LEU L 21 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE L 78 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE L 30 " --> pdb=" O CYS L 76 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS L 76 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 29 through 32 410 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2586 1.33 - 1.45: 4718 1.45 - 1.57: 6860 1.57 - 1.69: 602 1.69 - 1.81: 37 Bond restraints: 14803 Sorted by residual: bond pdb=" C GLY K 19 " pdb=" N PRO K 20 " ideal model delta sigma weight residual 1.331 1.344 -0.012 7.90e-03 1.60e+04 2.34e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CD M3L A 36 " pdb=" CE M3L A 36 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" N M3L A 36 " pdb=" CA M3L A 36 " ideal model delta sigma weight residual 1.458 1.441 0.017 1.90e-02 2.77e+03 8.47e-01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.99e-01 ... (remaining 14798 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.44: 752 103.44 - 111.09: 7168 111.09 - 118.74: 5186 118.74 - 126.39: 7201 126.39 - 134.05: 971 Bond angle restraints: 21278 Sorted by residual: angle pdb=" CB MET K 37 " pdb=" CG MET K 37 " pdb=" SD MET K 37 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA MET K 37 " pdb=" CB MET K 37 " pdb=" CG MET K 37 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C THR F 30 " pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 120.09 123.79 -3.70 1.25e+00 6.40e-01 8.78e+00 angle pdb=" CA GLU K 24 " pdb=" CB GLU K 24 " pdb=" CG GLU K 24 " ideal model delta sigma weight residual 114.10 119.14 -5.04 2.00e+00 2.50e-01 6.34e+00 angle pdb=" CG MET L 22 " pdb=" SD MET L 22 " pdb=" CE MET L 22 " ideal model delta sigma weight residual 100.90 95.78 5.12 2.20e+00 2.07e-01 5.41e+00 ... (remaining 21273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.03: 6354 31.03 - 62.05: 1732 62.05 - 93.08: 41 93.08 - 124.10: 0 124.10 - 155.13: 1 Dihedral angle restraints: 8128 sinusoidal: 5321 harmonic: 2807 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 64.87 155.13 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CB GLU L 124 " pdb=" CG GLU L 124 " pdb=" CD GLU L 124 " pdb=" OE1 GLU L 124 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA PHE L 17 " pdb=" C PHE L 17 " pdb=" N HIS L 18 " pdb=" CA HIS L 18 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1532 0.027 - 0.055: 598 0.055 - 0.082: 184 0.082 - 0.110: 62 0.110 - 0.137: 12 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE L 67 " pdb=" N ILE L 67 " pdb=" C ILE L 67 " pdb=" CB ILE L 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2385 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C GLU B 63 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.15e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 559 2.70 - 3.25: 11935 3.25 - 3.80: 26455 3.80 - 4.35: 33538 4.35 - 4.90: 47522 Nonbonded interactions: 120009 Sorted by model distance: nonbonded pdb=" O2 DC I 70 " pdb=" N2 DG J -70 " model vdw 2.155 2.496 nonbonded pdb=" OH TYR L 81 " pdb=" OE1 GLU L 90 " model vdw 2.175 2.440 nonbonded pdb=" O2 DC I -50 " pdb=" N2 DG J 50 " model vdw 2.194 2.496 nonbonded pdb=" O ALA K 99 " pdb=" ND2 ASN K 104 " model vdw 2.210 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.213 2.440 ... (remaining 120004 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 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 1.280 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: 6.180 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 44.220 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.003 0.038 14803 Z= 0.184 Angle : 0.567 11.427 21278 Z= 0.338 Chirality : 0.034 0.137 2388 Planarity : 0.005 0.042 1642 Dihedral : 26.984 155.126 6316 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.37 % Allowed : 14.62 % Favored : 85.01 % 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: 0.11 (0.26), residues: 940 helix: 1.01 (0.21), residues: 586 sheet: 0.29 (1.30), residues: 20 loop : -1.63 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 88 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE D 67 TYR 0.021 0.001 TYR L 23 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8329 (tttp) cc_final: 0.8125 (tttt) REVERT: D 105 LYS cc_start: 0.8014 (mtpm) cc_final: 0.7791 (mtpp) REVERT: H 44 GLN cc_start: 0.8067 (mt0) cc_final: 0.7730 (mt0) REVERT: K 37 MET cc_start: 0.3006 (ppp) cc_final: 0.2134 (tmm) REVERT: K 103 GLU cc_start: 0.3359 (pp20) cc_final: 0.2243 (tp30) REVERT: L 22 MET cc_start: 0.1646 (pmm) cc_final: 0.1049 (pmm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 1.9583 time to fit residues: 230.5533 Evaluate side-chains 102 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain K residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN K 80 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14803 Z= 0.303 Angle : 0.612 7.966 21278 Z= 0.359 Chirality : 0.039 0.140 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.216 156.942 4384 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.23 % Allowed : 14.62 % Favored : 83.15 % 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: 0.56 (0.26), residues: 940 helix: 1.39 (0.21), residues: 588 sheet: 0.36 (1.22), residues: 20 loop : -1.52 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 91 HIS 0.006 0.001 HIS E 39 PHE 0.011 0.002 PHE D 67 TYR 0.016 0.002 TYR L 23 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8055 (mttt) REVERT: G 41 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: H 44 GLN cc_start: 0.8064 (mt0) cc_final: 0.7764 (mt0) REVERT: K 37 MET cc_start: 0.2788 (ppp) cc_final: 0.1961 (tmm) REVERT: K 103 GLU cc_start: 0.3285 (pp20) cc_final: 0.2268 (tp30) REVERT: L 22 MET cc_start: 0.1286 (pmm) cc_final: 0.0986 (pmm) REVERT: L 94 TYR cc_start: 0.2614 (OUTLIER) cc_final: 0.1724 (t80) REVERT: E 120 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8543 (mtt) outliers start: 18 outliers final: 8 residues processed: 112 average time/residue: 1.9797 time to fit residues: 235.5161 Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14803 Z= 0.302 Angle : 0.608 8.056 21278 Z= 0.358 Chirality : 0.039 0.136 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.357 158.314 4384 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.47 % Allowed : 15.37 % Favored : 81.16 % 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: 0.84 (0.26), residues: 940 helix: 1.58 (0.21), residues: 588 sheet: 0.07 (0.75), residues: 40 loop : -1.39 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 91 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.002 PHE D 67 TYR 0.013 0.002 TYR L 23 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8080 (mttt) REVERT: G 35 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7618 (mtp-110) REVERT: G 41 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: H 44 GLN cc_start: 0.8065 (mt0) cc_final: 0.7859 (mt0) REVERT: K 108 LYS cc_start: 0.1191 (OUTLIER) cc_final: 0.0516 (mtmp) REVERT: L 22 MET cc_start: 0.1509 (pmm) cc_final: 0.1176 (pmm) REVERT: L 94 TYR cc_start: 0.2702 (OUTLIER) cc_final: 0.1792 (t80) REVERT: E 120 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8520 (mtt) outliers start: 28 outliers final: 11 residues processed: 115 average time/residue: 1.8920 time to fit residues: 231.1841 Evaluate side-chains 115 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14803 Z= 0.211 Angle : 0.577 7.906 21278 Z= 0.343 Chirality : 0.036 0.176 2388 Planarity : 0.004 0.050 1642 Dihedral : 30.327 157.998 4384 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.85 % Allowed : 16.48 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 940 helix: 1.81 (0.21), residues: 588 sheet: 0.39 (0.78), residues: 40 loop : -1.31 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE K 17 TYR 0.011 0.002 TYR L 23 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: D 65 ASP cc_start: 0.8805 (t0) cc_final: 0.8597 (t0) REVERT: G 41 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: H 31 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7096 (mmpt) REVERT: K 108 LYS cc_start: 0.1199 (OUTLIER) cc_final: 0.0519 (mtmp) REVERT: L 22 MET cc_start: 0.1384 (pmm) cc_final: 0.1019 (pmm) REVERT: L 94 TYR cc_start: 0.2654 (OUTLIER) cc_final: 0.1752 (t80) REVERT: E 120 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8478 (mtt) outliers start: 23 outliers final: 12 residues processed: 109 average time/residue: 1.8567 time to fit residues: 215.7999 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14803 Z= 0.269 Angle : 0.586 7.685 21278 Z= 0.348 Chirality : 0.037 0.131 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.266 157.993 4384 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.10 % Allowed : 16.60 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 940 helix: 1.79 (0.21), residues: 588 sheet: 1.19 (1.17), residues: 20 loop : -1.29 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 91 HIS 0.004 0.001 HIS E 39 PHE 0.008 0.001 PHE D 67 TYR 0.013 0.002 TYR D 118 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7860 (mtt-85) REVERT: C 74 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: G 35 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7606 (mtp-110) REVERT: G 41 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: H 31 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7113 (mmpt) REVERT: H 44 GLN cc_start: 0.8113 (mt0) cc_final: 0.7868 (mt0) REVERT: K 108 LYS cc_start: 0.1224 (OUTLIER) cc_final: 0.0520 (mtmp) REVERT: L 22 MET cc_start: 0.1405 (pmm) cc_final: 0.1081 (pmm) REVERT: L 94 TYR cc_start: 0.2651 (OUTLIER) cc_final: 0.1757 (t80) REVERT: E 90 MET cc_start: 0.7686 (mmm) cc_final: 0.7426 (mmm) REVERT: E 120 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8522 (mtt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 1.9376 time to fit residues: 230.5330 Evaluate side-chains 118 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14803 Z= 0.188 Angle : 0.567 7.617 21278 Z= 0.338 Chirality : 0.035 0.133 2388 Planarity : 0.004 0.047 1642 Dihedral : 30.245 157.554 4384 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.73 % Allowed : 17.35 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 940 helix: 1.96 (0.21), residues: 588 sheet: 0.85 (0.78), residues: 40 loop : -1.21 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 91 HIS 0.002 0.001 HIS L 80 PHE 0.008 0.001 PHE D 67 TYR 0.010 0.001 TYR D 118 ARG 0.010 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7795 (mtt-85) REVERT: D 65 ASP cc_start: 0.8800 (t0) cc_final: 0.8593 (t0) REVERT: G 41 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: H 31 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7137 (mmpt) REVERT: H 44 GLN cc_start: 0.8062 (mt0) cc_final: 0.7744 (mt0) REVERT: K 108 LYS cc_start: 0.1258 (OUTLIER) cc_final: 0.0533 (mtmp) REVERT: L 22 MET cc_start: 0.1148 (pmm) cc_final: 0.0884 (pmm) REVERT: L 94 TYR cc_start: 0.2640 (OUTLIER) cc_final: 0.1748 (t80) REVERT: E 90 MET cc_start: 0.7650 (mmm) cc_final: 0.7392 (mmm) REVERT: E 120 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8459 (mtt) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 1.9161 time to fit residues: 221.8569 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 14803 Z= 0.438 Angle : 0.691 7.651 21278 Z= 0.399 Chirality : 0.045 0.168 2388 Planarity : 0.006 0.056 1642 Dihedral : 30.641 158.566 4384 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.97 % Allowed : 16.11 % Favored : 79.93 % 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: 0.74 (0.26), residues: 940 helix: 1.43 (0.21), residues: 590 sheet: 0.76 (0.78), residues: 40 loop : -1.38 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 91 HIS 0.008 0.002 HIS E 39 PHE 0.012 0.002 PHE F 100 TYR 0.019 0.003 TYR D 118 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7954 (mtt-85) REVERT: C 74 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8095 (mttt) REVERT: G 35 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7647 (mtp-110) REVERT: G 41 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: H 31 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7138 (mmpt) REVERT: H 44 GLN cc_start: 0.8039 (mt0) cc_final: 0.7744 (mt0) REVERT: K 70 GLU cc_start: 0.2797 (OUTLIER) cc_final: 0.0628 (tp30) REVERT: K 108 LYS cc_start: 0.1272 (OUTLIER) cc_final: 0.0576 (mtmp) REVERT: L 94 TYR cc_start: 0.2757 (OUTLIER) cc_final: 0.2207 (t80) REVERT: E 90 MET cc_start: 0.7704 (mmm) cc_final: 0.7461 (mmm) REVERT: E 120 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8569 (mtt) outliers start: 32 outliers final: 16 residues processed: 119 average time/residue: 1.9556 time to fit residues: 247.2058 Evaluate side-chains 123 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14803 Z= 0.222 Angle : 0.605 7.833 21278 Z= 0.360 Chirality : 0.038 0.132 2388 Planarity : 0.005 0.049 1642 Dihedral : 30.595 157.659 4384 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.85 % Allowed : 17.60 % Favored : 79.55 % 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: 1.06 (0.27), residues: 940 helix: 1.71 (0.21), residues: 589 sheet: 0.74 (0.76), residues: 40 loop : -1.31 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 91 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.001 PHE D 67 TYR 0.013 0.002 TYR D 118 ARG 0.008 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7816 (mtt-85) REVERT: C 74 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8179 (mttt) REVERT: D 105 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7968 (mttt) REVERT: H 31 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7151 (mmpt) REVERT: H 44 GLN cc_start: 0.8008 (mt0) cc_final: 0.7724 (mt0) REVERT: K 108 LYS cc_start: 0.1300 (OUTLIER) cc_final: 0.0568 (mtmp) REVERT: E 90 MET cc_start: 0.7666 (mmm) cc_final: 0.7407 (mmm) REVERT: E 120 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8492 (mtt) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 1.8903 time to fit residues: 223.0757 Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14803 Z= 0.279 Angle : 0.611 7.567 21278 Z= 0.360 Chirality : 0.038 0.136 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.477 158.271 4384 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.73 % Allowed : 17.84 % Favored : 79.43 % 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: 1.07 (0.27), residues: 940 helix: 1.72 (0.21), residues: 589 sheet: 0.68 (0.76), residues: 40 loop : -1.29 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 91 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.002 PHE H 62 TYR 0.015 0.002 TYR D 118 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8130 (mttt) REVERT: G 35 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7599 (mtp-110) REVERT: H 31 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7113 (mmpt) REVERT: H 44 GLN cc_start: 0.8009 (mt0) cc_final: 0.7751 (mt0) REVERT: K 70 GLU cc_start: 0.2780 (OUTLIER) cc_final: 0.0614 (tp30) REVERT: K 108 LYS cc_start: 0.1100 (OUTLIER) cc_final: 0.0520 (mtmp) REVERT: L 94 TYR cc_start: 0.2683 (OUTLIER) cc_final: 0.2139 (t80) REVERT: E 90 MET cc_start: 0.7718 (mmm) cc_final: 0.7458 (mmm) REVERT: E 120 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8496 (mtt) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 1.9559 time to fit residues: 222.3102 Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14803 Z= 0.271 Angle : 0.603 8.089 21278 Z= 0.357 Chirality : 0.038 0.134 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.463 158.444 4384 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.60 % Allowed : 17.97 % Favored : 79.43 % 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: 1.09 (0.27), residues: 940 helix: 1.73 (0.21), residues: 589 sheet: 0.68 (0.76), residues: 40 loop : -1.28 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS L 80 PHE 0.008 0.001 PHE D 67 TYR 0.016 0.002 TYR D 118 ARG 0.010 0.001 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8130 (mttt) REVERT: G 35 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7599 (mtp-110) REVERT: H 31 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7110 (mmpt) REVERT: H 44 GLN cc_start: 0.8031 (mt0) cc_final: 0.7746 (mt0) REVERT: K 70 GLU cc_start: 0.2777 (OUTLIER) cc_final: 0.0619 (tp30) REVERT: K 108 LYS cc_start: 0.1092 (OUTLIER) cc_final: 0.0529 (mtmp) REVERT: L 94 TYR cc_start: 0.2679 (OUTLIER) cc_final: 0.2136 (t80) REVERT: E 90 MET cc_start: 0.7718 (mmm) cc_final: 0.7457 (mmm) REVERT: E 120 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8522 (mtt) outliers start: 21 outliers final: 14 residues processed: 106 average time/residue: 1.9119 time to fit residues: 215.2607 Evaluate side-chains 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095326 restraints weight = 19583.456| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.05 r_work: 0.2906 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14803 Z= 0.163 Angle : 0.569 7.333 21278 Z= 0.341 Chirality : 0.035 0.136 2388 Planarity : 0.004 0.047 1642 Dihedral : 30.387 157.506 4384 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 18.71 % Favored : 79.31 % 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: 1.52 (0.27), residues: 940 helix: 2.10 (0.21), residues: 588 sheet: 0.77 (0.77), residues: 40 loop : -1.15 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE F 61 TYR 0.010 0.001 TYR B 51 ARG 0.009 0.001 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.41 seconds wall clock time: 80 minutes 29.80 seconds (4829.80 seconds total)