Starting phenix.real_space_refine on Sat Mar 16 02:11:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pep_17634/03_2024/8pep_17634_updated.pdb" } resolution = 3.33 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= 0.011 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 7599 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 73": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" 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: 13492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 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: {'M2L: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: "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: "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: 7.28, per 1000 atoms: 0.54 Number of scatterers: 13492 At special positions: 0 Unit cell: (95.019, 120.024, 138.361, 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 7599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.53 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 52.8% alpha, 3.8% beta 135 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.934A 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: 3.742A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.551A 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 37 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: 4.515A 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: 4.249A 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: 4.109A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.638A 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: 4.330A 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 81 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.554A 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: 4.040A 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: 3.750A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3179 1.34 - 1.46: 4341 1.46 - 1.58: 6223 1.58 - 1.70: 584 1.70 - 1.82: 30 Bond restraints: 14357 Sorted by residual: bond pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C M2L A 36 " pdb=" O M2L A 36 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C3' DG J 63 " pdb=" O3' DG J 63 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.62e-02 3.81e+03 1.70e+00 ... (remaining 14352 not shown) Histogram of bond angle deviations from ideal: 95.03 - 102.82: 515 102.82 - 110.62: 6013 110.62 - 118.41: 5932 118.41 - 126.20: 7215 126.20 - 134.00: 944 Bond angle restraints: 20619 Sorted by residual: angle pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " pdb=" CD LYS K 65 " ideal model delta sigma weight residual 111.30 124.90 -13.60 2.30e+00 1.89e-01 3.50e+01 angle pdb=" CA LYS K 65 " pdb=" CB LYS K 65 " pdb=" CG LYS K 65 " ideal model delta sigma weight residual 114.10 125.68 -11.58 2.00e+00 2.50e-01 3.35e+01 angle pdb=" C MET L 1 " pdb=" CA MET L 1 " pdb=" CB MET L 1 " ideal model delta sigma weight residual 110.10 118.38 -8.28 1.90e+00 2.77e-01 1.90e+01 angle pdb=" C LYS K 65 " pdb=" CA LYS K 65 " pdb=" CB LYS K 65 " ideal model delta sigma weight residual 110.79 104.32 6.47 1.66e+00 3.63e-01 1.52e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 122.07 127.27 -5.20 1.43e+00 4.89e-01 1.32e+01 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 6267 35.32 - 70.63: 1598 70.63 - 105.95: 41 105.95 - 141.26: 3 141.26 - 176.58: 4 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" CD M2L A 36 " pdb=" CE M2L A 36 " pdb=" NZ M2L A 36 " pdb=" CM1 M2L A 36 " ideal model delta sinusoidal sigma weight residual 66.23 -97.70 163.93 1 3.00e+01 1.11e-03 2.09e+01 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 43.42 176.58 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 24.58 -164.58 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1969 0.061 - 0.123: 319 0.123 - 0.184: 26 0.184 - 0.245: 6 0.245 - 0.307: 2 Chirality restraints: 2322 Sorted by residual: 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 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS K 65 " pdb=" N LYS K 65 " pdb=" C LYS K 65 " pdb=" CB LYS K 65 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ARG F 23 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 114 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ALA D 114 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA D 114 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL D 115 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 55 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG F 55 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG F 55 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY F 56 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 248 2.65 - 3.22: 11217 3.22 - 3.78: 24860 3.78 - 4.34: 32190 4.34 - 4.90: 46641 Nonbonded interactions: 115156 Sorted by model distance: nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.092 2.440 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.100 2.520 nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.222 2.520 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.235 2.520 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.244 2.520 ... (remaining 115151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.400 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 45.370 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.050 14357 Z= 0.211 Angle : 0.716 13.598 20619 Z= 0.422 Chirality : 0.045 0.307 2322 Planarity : 0.007 0.086 1605 Dihedral : 28.764 176.578 6157 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % 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: 0.85 (0.27), residues: 913 helix: 1.74 (0.22), residues: 548 sheet: -2.95 (0.69), residues: 34 loop : -1.06 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 21 HIS 0.007 0.001 HIS L 20 PHE 0.036 0.002 PHE C 25 TYR 0.035 0.002 TYR K 61 ARG 0.022 0.001 ARG E 129 *********************** 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 158 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8596 (mtmm) REVERT: G 38 ASN cc_start: 0.7909 (m-40) cc_final: 0.7453 (m-40) REVERT: K 52 PHE cc_start: 0.8284 (m-10) cc_final: 0.8077 (m-80) REVERT: K 78 ASN cc_start: 0.9218 (m-40) cc_final: 0.8985 (m-40) REVERT: L 20 HIS cc_start: 0.7653 (m-70) cc_final: 0.7016 (m170) REVERT: L 59 PHE cc_start: 0.8454 (m-80) cc_final: 0.7894 (m-80) REVERT: L 77 PHE cc_start: 0.8300 (t80) cc_final: 0.7713 (t80) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.3936 time to fit residues: 79.5288 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14357 Z= 0.175 Angle : 0.574 9.219 20619 Z= 0.335 Chirality : 0.035 0.186 2322 Planarity : 0.005 0.040 1605 Dihedral : 31.195 178.719 4250 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % 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: 1.15 (0.28), residues: 913 helix: 1.91 (0.22), residues: 554 sheet: -2.48 (0.73), residues: 36 loop : -0.87 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 82 HIS 0.005 0.001 HIS G 31 PHE 0.011 0.001 PHE C 25 TYR 0.027 0.001 TYR L 61 ARG 0.008 0.001 ARG G 35 *********************** 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 104 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.8329 (tpp) cc_final: 0.7606 (tpp) REVERT: E 39 HIS cc_start: 0.7101 (t-90) cc_final: 0.6704 (m170) REVERT: E 56 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8543 (mtmm) REVERT: K 1 MET cc_start: 0.2374 (ptp) cc_final: 0.1466 (pmm) REVERT: K 53 LEU cc_start: 0.8862 (tt) cc_final: 0.8509 (mp) REVERT: K 78 ASN cc_start: 0.9190 (m-40) cc_final: 0.8618 (p0) REVERT: L 20 HIS cc_start: 0.7787 (m90) cc_final: 0.7425 (m90) REVERT: L 40 LEU cc_start: 0.7472 (tp) cc_final: 0.7095 (tt) REVERT: L 77 PHE cc_start: 0.8072 (t80) cc_final: 0.7669 (t80) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.3323 time to fit residues: 46.6114 Evaluate side-chains 81 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 46 HIS F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 14357 Z= 0.387 Angle : 0.634 7.008 20619 Z= 0.368 Chirality : 0.039 0.180 2322 Planarity : 0.005 0.032 1605 Dihedral : 31.003 167.496 4250 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.63 % Allowed : 11.79 % Favored : 87.58 % 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: 0.77 (0.27), residues: 913 helix: 1.50 (0.22), residues: 569 sheet: -2.21 (0.75), residues: 41 loop : -0.95 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 82 HIS 0.006 0.002 HIS D 79 PHE 0.055 0.002 PHE L 59 TYR 0.015 0.002 TYR D 80 ARG 0.006 0.001 ARG D 76 *********************** 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 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.988 Fit side-chains REVERT: A 125 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7202 (mm-40) REVERT: D 31 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8899 (mmmm) REVERT: F 24 ASP cc_start: 0.8299 (p0) cc_final: 0.8061 (p0) REVERT: K 1 MET cc_start: 0.3009 (ptp) cc_final: 0.1868 (pmm) REVERT: K 15 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (ptm) REVERT: K 78 ASN cc_start: 0.9223 (m-40) cc_final: 0.8927 (p0) REVERT: L 59 PHE cc_start: 0.9307 (t80) cc_final: 0.9056 (t80) REVERT: L 77 PHE cc_start: 0.8324 (t80) cc_final: 0.7431 (t80) REVERT: L 82 TRP cc_start: 0.8511 (m100) cc_final: 0.8268 (m100) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.3349 time to fit residues: 39.0203 Evaluate side-chains 82 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 86 ASN 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: 5.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.0050 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14357 Z= 0.245 Angle : 0.561 9.216 20619 Z= 0.329 Chirality : 0.035 0.166 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.667 165.201 4250 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.51 % Allowed : 12.93 % 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: 1.12 (0.28), residues: 913 helix: 1.83 (0.22), residues: 563 sheet: -1.88 (0.68), residues: 50 loop : -0.88 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 82 HIS 0.004 0.001 HIS D 106 PHE 0.016 0.001 PHE L 59 TYR 0.010 0.001 TYR G 50 ARG 0.008 0.000 ARG D 76 *********************** 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 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8095 (p0) cc_final: 0.7746 (p0) REVERT: D 31 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8874 (mmmm) REVERT: D 56 MET cc_start: 0.8606 (tpp) cc_final: 0.7920 (tpp) REVERT: K 15 MET cc_start: 0.8037 (ppp) cc_final: 0.7016 (ptp) REVERT: K 53 LEU cc_start: 0.9133 (tt) cc_final: 0.8624 (mp) REVERT: K 78 ASN cc_start: 0.9347 (m-40) cc_final: 0.8936 (p0) REVERT: L 59 PHE cc_start: 0.9063 (t80) cc_final: 0.8755 (t80) REVERT: L 77 PHE cc_start: 0.8202 (t80) cc_final: 0.7131 (t80) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.3689 time to fit residues: 44.4723 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14357 Z= 0.263 Angle : 0.564 8.353 20619 Z= 0.330 Chirality : 0.035 0.168 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.569 171.379 4250 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.39 % Allowed : 14.07 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 913 helix: 1.96 (0.22), residues: 565 sheet: -1.81 (0.79), residues: 41 loop : -0.85 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 82 HIS 0.004 0.001 HIS D 106 PHE 0.017 0.001 PHE C 25 TYR 0.009 0.001 TYR G 50 ARG 0.011 0.000 ARG D 76 *********************** 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 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8861 (mmmm) REVERT: D 56 MET cc_start: 0.8644 (tpp) cc_final: 0.8071 (tpp) REVERT: E 59 GLU cc_start: 0.8103 (pp20) cc_final: 0.7813 (pp20) REVERT: K 1 MET cc_start: 0.3348 (ptp) cc_final: 0.2673 (pmm) REVERT: K 15 MET cc_start: 0.8022 (ppp) cc_final: 0.7020 (ptt) REVERT: K 53 LEU cc_start: 0.9158 (tt) cc_final: 0.8658 (mp) REVERT: K 78 ASN cc_start: 0.9352 (m-40) cc_final: 0.9044 (p0) REVERT: L 77 PHE cc_start: 0.8241 (t80) cc_final: 0.7154 (t80) outliers start: 11 outliers final: 6 residues processed: 91 average time/residue: 0.3152 time to fit residues: 38.9405 Evaluate side-chains 83 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 20 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS F 75 HIS ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14357 Z= 0.210 Angle : 0.544 7.610 20619 Z= 0.320 Chirality : 0.034 0.159 2322 Planarity : 0.004 0.045 1605 Dihedral : 30.489 175.795 4250 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.01 % Allowed : 14.70 % Favored : 84.28 % 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: 1.50 (0.28), residues: 913 helix: 2.13 (0.22), residues: 563 sheet: -1.46 (0.83), residues: 41 loop : -0.81 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 82 HIS 0.004 0.001 HIS F 75 PHE 0.034 0.001 PHE L 59 TYR 0.007 0.001 TYR B 88 ARG 0.012 0.000 ARG D 76 *********************** 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 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.162 Fit side-chains REVERT: D 56 MET cc_start: 0.8671 (tpp) cc_final: 0.8023 (tpp) REVERT: E 56 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8718 (mtmm) REVERT: E 59 GLU cc_start: 0.8025 (pp20) cc_final: 0.7774 (pp20) REVERT: K 15 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6755 (ppp) REVERT: K 53 LEU cc_start: 0.9127 (tt) cc_final: 0.8708 (mp) REVERT: K 78 ASN cc_start: 0.9361 (m-40) cc_final: 0.9065 (p0) REVERT: L 20 HIS cc_start: 0.5185 (OUTLIER) cc_final: 0.4982 (t-90) REVERT: L 59 PHE cc_start: 0.8408 (t80) cc_final: 0.8181 (t80) REVERT: L 77 PHE cc_start: 0.8139 (t80) cc_final: 0.7032 (t80) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 0.3387 time to fit residues: 42.0627 Evaluate side-chains 87 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain L residue 20 HIS Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 92 GLN E 39 HIS F 75 HIS K 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14357 Z= 0.268 Angle : 0.567 6.998 20619 Z= 0.331 Chirality : 0.035 0.166 2322 Planarity : 0.004 0.045 1605 Dihedral : 30.537 178.760 4250 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 14.96 % Favored : 83.40 % 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: 1.51 (0.28), residues: 913 helix: 2.08 (0.22), residues: 564 sheet: -1.52 (0.80), residues: 43 loop : -0.66 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 82 HIS 0.003 0.001 HIS B 75 PHE 0.021 0.001 PHE L 59 TYR 0.009 0.001 TYR C 50 ARG 0.013 0.000 ARG D 76 *********************** 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: 13 poor density : 86 time to evaluate : 1.099 Fit side-chains REVERT: D 56 MET cc_start: 0.8725 (tpp) cc_final: 0.7957 (tpp) REVERT: E 56 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8753 (mtmm) REVERT: K 15 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6931 (ppp) REVERT: K 53 LEU cc_start: 0.9179 (tt) cc_final: 0.8755 (mp) REVERT: K 78 ASN cc_start: 0.9380 (m-40) cc_final: 0.9108 (p0) REVERT: L 52 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8069 (t80) REVERT: L 59 PHE cc_start: 0.8463 (t80) cc_final: 0.8230 (t80) REVERT: L 77 PHE cc_start: 0.8067 (t80) cc_final: 0.6882 (t80) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 0.3193 time to fit residues: 40.2755 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 86 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 89 ASN E 39 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14357 Z= 0.189 Angle : 0.553 7.767 20619 Z= 0.322 Chirality : 0.034 0.154 2322 Planarity : 0.004 0.052 1605 Dihedral : 30.341 178.094 4250 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 15.72 % Favored : 83.40 % 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: 1.75 (0.28), residues: 913 helix: 2.26 (0.22), residues: 562 sheet: -1.37 (0.86), residues: 38 loop : -0.55 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.018 0.001 PHE L 59 TYR 0.009 0.001 TYR L 61 ARG 0.013 0.000 ARG D 76 *********************** 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 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.126 Fit side-chains REVERT: D 56 MET cc_start: 0.8661 (tpp) cc_final: 0.7995 (tpp) REVERT: E 56 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8782 (mtmm) REVERT: K 15 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6650 (ppp) REVERT: K 53 LEU cc_start: 0.9142 (tt) cc_final: 0.8746 (mp) REVERT: K 78 ASN cc_start: 0.9348 (m-40) cc_final: 0.9085 (p0) REVERT: L 20 HIS cc_start: 0.5339 (t-90) cc_final: 0.5103 (t-170) REVERT: L 52 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8188 (t80) REVERT: L 59 PHE cc_start: 0.8248 (t80) cc_final: 0.7999 (t80) REVERT: L 77 PHE cc_start: 0.8115 (t80) cc_final: 0.7147 (t80) outliers start: 7 outliers final: 2 residues processed: 90 average time/residue: 0.3139 time to fit residues: 38.8428 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 PHE 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: 4.9990 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14357 Z= 0.356 Angle : 0.623 9.246 20619 Z= 0.357 Chirality : 0.037 0.150 2322 Planarity : 0.005 0.050 1605 Dihedral : 30.572 172.049 4250 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.01 % Allowed : 15.97 % Favored : 83.02 % 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: 1.43 (0.28), residues: 913 helix: 1.94 (0.22), residues: 564 sheet: -1.34 (0.86), residues: 38 loop : -0.59 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.002 PHE C 25 TYR 0.012 0.002 TYR C 50 ARG 0.012 0.001 ARG D 76 *********************** 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 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.134 Fit side-chains REVERT: D 56 MET cc_start: 0.8768 (tpp) cc_final: 0.7992 (tpp) REVERT: K 15 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: K 78 ASN cc_start: 0.9398 (m-40) cc_final: 0.9154 (p0) REVERT: L 52 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7961 (t80) REVERT: L 59 PHE cc_start: 0.7517 (t80) cc_final: 0.7302 (t80) REVERT: L 77 PHE cc_start: 0.8135 (t80) cc_final: 0.7094 (t80) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.3417 time to fit residues: 40.2100 Evaluate side-chains 83 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 PHE 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: 0.6980 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14357 Z= 0.208 Angle : 0.574 8.967 20619 Z= 0.332 Chirality : 0.034 0.160 2322 Planarity : 0.004 0.048 1605 Dihedral : 30.371 175.431 4250 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 16.22 % Favored : 82.89 % 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: 1.60 (0.28), residues: 913 helix: 2.12 (0.22), residues: 561 sheet: -1.39 (0.85), residues: 38 loop : -0.56 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP L 82 HIS 0.010 0.001 HIS L 20 PHE 0.013 0.001 PHE L 59 TYR 0.008 0.001 TYR H 37 ARG 0.011 0.000 ARG D 76 ********************** 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 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.156 Fit side-chains REVERT: D 56 MET cc_start: 0.8698 (tpp) cc_final: 0.8046 (tpp) REVERT: K 15 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.6947 (ppp) REVERT: K 78 ASN cc_start: 0.9370 (m-40) cc_final: 0.9116 (p0) REVERT: L 20 HIS cc_start: 0.5542 (t-90) cc_final: 0.5332 (t-90) REVERT: L 52 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7971 (t80) REVERT: L 77 PHE cc_start: 0.8237 (t80) cc_final: 0.7280 (t80) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 0.3210 time to fit residues: 39.1039 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 PHE 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: 6.9990 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 39 HIS F 75 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.062486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040461 restraints weight = 65058.818| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.94 r_work: 0.2586 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14357 Z= 0.201 Angle : 0.566 9.056 20619 Z= 0.327 Chirality : 0.034 0.183 2322 Planarity : 0.004 0.050 1605 Dihedral : 30.293 175.761 4250 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.76 % Allowed : 16.35 % Favored : 82.89 % 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: 1.75 (0.28), residues: 913 helix: 2.23 (0.22), residues: 561 sheet: -1.37 (0.85), residues: 38 loop : -0.47 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 82 HIS 0.005 0.001 HIS L 20 PHE 0.019 0.001 PHE L 59 TYR 0.032 0.001 TYR L 61 ARG 0.011 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.67 seconds wall clock time: 46 minutes 36.13 seconds (2796.13 seconds total)