Starting phenix.real_space_refine on Tue Feb 13 10:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a04_15047/02_2024/8a04_15047.pdb" } resolution = 3.2 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= 0.016 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 72": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 220": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "H" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "G" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.54, per 1000 atoms: 0.64 Number of scatterers: 5511 At special positions: 0 Unit cell: (96.72, 95.48, 66.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 10.7% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'I' and resid 31 through 35 removed outlier: 3.711A pdb=" N LEU I 35 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 178 through 190 removed outlier: 3.855A pdb=" N ILE I 189 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.546A pdb=" N LEU H 35 " --> pdb=" O LEU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 178 through 190 removed outlier: 3.934A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 35 removed outlier: 3.529A pdb=" N LEU G 35 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.507A pdb=" N SER G 67 " --> pdb=" O PHE G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 190 removed outlier: 3.557A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 2 through 7 removed outlier: 5.766A pdb=" N LYS I 2 " --> pdb=" O GLY I 119 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY I 119 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA I 4 " --> pdb=" O LEU I 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 15 through 17 removed outlier: 6.981A pdb=" N ILE I 40 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN I 56 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE I 42 " --> pdb=" O LEU I 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 93 through 94 removed outlier: 5.602A pdb=" N SER I 93 " --> pdb=" O THR I 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 128 through 137 removed outlier: 5.314A pdb=" N ASN I 230 " --> pdb=" O THR I 157 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU I 153 " --> pdb=" O ARG I 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 143 through 146 removed outlier: 3.505A pdb=" N GLY I 218 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 7 removed outlier: 5.522A pdb=" N LYS H 2 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY H 119 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA H 4 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 15 through 17 removed outlier: 7.189A pdb=" N ILE H 40 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN H 56 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE H 42 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 93 through 94 removed outlier: 5.604A pdb=" N SER H 93 " --> pdb=" O THR H 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 128 through 137 removed outlier: 5.435A pdb=" N ASN H 230 " --> pdb=" O THR H 157 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU H 153 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 7 removed outlier: 5.975A pdb=" N LYS G 2 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY G 119 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 4 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 15 through 17 removed outlier: 3.621A pdb=" N SER G 101 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE G 40 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN G 56 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE G 42 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 93 through 94 removed outlier: 5.135A pdb=" N SER G 93 " --> pdb=" O THR G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 128 through 137 removed outlier: 5.144A pdb=" N ASN G 230 " --> pdb=" O THR G 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU G 153 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU G 236 " --> pdb=" O PHE G 151 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE G 151 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 143 through 147 removed outlier: 6.525A pdb=" N GLN G 168 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE G 219 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER G 166 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE G 221 " --> pdb=" O ASP G 164 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP G 164 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS G 223 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL G 162 " --> pdb=" O LYS G 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 194 through 195 221 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 914 1.46 - 1.57: 2815 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" N GLY I 92 " pdb=" CA GLY I 92 " ideal model delta sigma weight residual 1.458 1.447 0.011 9.20e-03 1.18e+04 1.31e+00 bond pdb=" C LYS G 11 " pdb=" N SER G 12 " ideal model delta sigma weight residual 1.335 1.305 0.029 3.04e-02 1.08e+03 9.20e-01 bond pdb=" CB GLU G 220 " pdb=" CG GLU G 220 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.49e-01 bond pdb=" CA GLU G 220 " pdb=" C GLU G 220 " ideal model delta sigma weight residual 1.522 1.512 0.010 1.20e-02 6.94e+03 6.46e-01 bond pdb=" CG GLU I 100 " pdb=" CD GLU I 100 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.74e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.31: 67 106.31 - 112.55: 3039 112.55 - 118.78: 1558 118.78 - 125.02: 2860 125.02 - 131.26: 24 Bond angle restraints: 7548 Sorted by residual: angle pdb=" N GLY G 49 " pdb=" CA GLY G 49 " pdb=" C GLY G 49 " ideal model delta sigma weight residual 111.36 115.41 -4.05 1.17e+00 7.31e-01 1.20e+01 angle pdb=" C VAL H 202 " pdb=" N GLN H 203 " pdb=" CA GLN H 203 " ideal model delta sigma weight residual 120.68 125.26 -4.58 1.70e+00 3.46e-01 7.25e+00 angle pdb=" N ASP I 98 " pdb=" CA ASP I 98 " pdb=" C ASP I 98 " ideal model delta sigma weight residual 111.71 114.29 -2.58 1.15e+00 7.56e-01 5.03e+00 angle pdb=" C ASN G 48 " pdb=" N GLY G 49 " pdb=" CA GLY G 49 " ideal model delta sigma weight residual 119.92 121.96 -2.04 9.60e-01 1.09e+00 4.53e+00 angle pdb=" C GLY G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.40e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3091 17.81 - 35.62: 260 35.62 - 53.43: 47 53.43 - 71.25: 17 71.25 - 89.06: 5 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA ALA I 97 " pdb=" C ALA I 97 " pdb=" N ASP I 98 " pdb=" CA ASP I 98 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ASP G 108 " pdb=" CB ASP G 108 " pdb=" CG ASP G 108 " pdb=" OD1 ASP G 108 " ideal model delta sinusoidal sigma weight residual -30.00 -83.06 53.06 1 2.00e+01 2.50e-03 9.58e+00 dihedral pdb=" CA ARG I 114 " pdb=" CB ARG I 114 " pdb=" CG ARG I 114 " pdb=" CD ARG I 114 " ideal model delta sinusoidal sigma weight residual -60.00 -116.58 56.58 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 556 0.031 - 0.061: 214 0.061 - 0.092: 76 0.092 - 0.122: 69 0.122 - 0.153: 21 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE H 155 " pdb=" N ILE H 155 " pdb=" C ILE H 155 " pdb=" CB ILE H 155 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE I 42 " pdb=" N ILE I 42 " pdb=" C ILE I 42 " pdb=" CB ILE I 42 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE H 42 " pdb=" N ILE H 42 " pdb=" C ILE H 42 " pdb=" CB ILE H 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 178 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO H 179 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO H 179 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 179 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 178 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.48e-01 pdb=" N PRO G 179 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO G 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 179 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 190 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.25e-01 pdb=" N PRO H 191 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 191 " 0.013 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 67 2.67 - 3.23: 4716 3.23 - 3.79: 7425 3.79 - 4.34: 10788 4.34 - 4.90: 19056 Nonbonded interactions: 42052 Sorted by model distance: nonbonded pdb=" OD2 ASP H 159 " pdb=" OG SER H 227 " model vdw 2.113 2.440 nonbonded pdb=" OD2 ASP G 190 " pdb=" NE2 GLN G 193 " model vdw 2.305 2.520 nonbonded pdb=" OD1 ASP H 159 " pdb=" N ASP H 160 " model vdw 2.346 2.520 nonbonded pdb=" OD1 ASN G 128 " pdb=" OG1 THR G 238 " model vdw 2.379 2.440 nonbonded pdb=" OD1 ASP H 77 " pdb=" N ALA H 78 " model vdw 2.385 2.520 ... (remaining 42047 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 'G' selection = chain 'H' selection = chain 'I' } 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=1.00 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: 0.530 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: 2.110 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.780 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 0.040 5571 Z= 0.245 Angle : 0.599 4.576 7548 Z= 0.346 Chirality : 0.048 0.153 936 Planarity : 0.003 0.025 960 Dihedral : 14.528 89.057 2064 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.52 (0.31), residues: 711 helix: 0.46 (0.68), residues: 66 sheet: 0.50 (0.33), residues: 261 loop : -1.10 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 118 PHE 0.012 0.001 PHE H 231 TYR 0.013 0.001 TYR G 43 ARG 0.005 0.001 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: I 53 ILE cc_start: 0.8893 (mp) cc_final: 0.8544 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1590 time to fit residues: 23.0024 Evaluate side-chains 74 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 80 ASN H 193 GLN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5571 Z= 0.210 Angle : 0.502 4.251 7548 Z= 0.277 Chirality : 0.047 0.147 936 Planarity : 0.003 0.026 960 Dihedral : 4.087 15.384 750 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.75 % Allowed : 7.46 % Favored : 90.79 % 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: -0.20 (0.32), residues: 711 helix: 0.94 (0.69), residues: 63 sheet: 0.75 (0.30), residues: 306 loop : -1.19 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 118 PHE 0.011 0.001 PHE I 231 TYR 0.013 0.001 TYR G 43 ARG 0.002 0.000 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.707 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.1592 time to fit residues: 18.4431 Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 75 GLN I 80 ASN I 225 GLN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5571 Z= 0.326 Angle : 0.554 4.531 7548 Z= 0.302 Chirality : 0.048 0.152 936 Planarity : 0.003 0.028 960 Dihedral : 4.331 15.754 750 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 12.38 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.32), residues: 711 helix: 0.66 (0.69), residues: 63 sheet: 0.19 (0.29), residues: 351 loop : -1.24 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.013 0.001 PHE H 231 TYR 0.016 0.001 TYR G 43 ARG 0.003 0.001 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.624 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 85 average time/residue: 0.1463 time to fit residues: 16.9609 Evaluate side-chains 82 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5571 Z= 0.232 Angle : 0.498 4.144 7548 Z= 0.275 Chirality : 0.047 0.141 936 Planarity : 0.003 0.028 960 Dihedral : 4.152 15.341 750 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.86 % Allowed : 13.02 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 711 helix: 0.78 (0.70), residues: 63 sheet: 0.64 (0.30), residues: 306 loop : -1.26 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.011 0.001 PHE H 231 TYR 0.015 0.001 TYR G 43 ARG 0.002 0.000 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.685 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 82 average time/residue: 0.1569 time to fit residues: 17.6801 Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 230 ASN Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 80 ASN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 5571 Z= 0.411 Angle : 0.602 5.116 7548 Z= 0.325 Chirality : 0.049 0.155 936 Planarity : 0.003 0.028 960 Dihedral : 4.582 16.572 750 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.33 % Allowed : 16.19 % Favored : 80.48 % 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: -0.68 (0.31), residues: 711 helix: 0.40 (0.68), residues: 63 sheet: 0.19 (0.29), residues: 336 loop : -1.32 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 118 PHE 0.014 0.002 PHE H 231 TYR 0.017 0.002 TYR G 43 ARG 0.004 0.001 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: G 188 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7592 (t70) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 0.1492 time to fit residues: 16.5778 Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5571 Z= 0.189 Angle : 0.475 4.108 7548 Z= 0.263 Chirality : 0.046 0.137 936 Planarity : 0.003 0.030 960 Dihedral : 4.068 14.458 750 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.17 % Allowed : 17.30 % Favored : 79.52 % 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: -0.41 (0.31), residues: 711 helix: 0.72 (0.70), residues: 63 sheet: 0.63 (0.30), residues: 306 loop : -1.33 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.009 0.001 PHE H 231 TYR 0.012 0.001 TYR G 43 ARG 0.002 0.000 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: G 188 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7584 (t70) outliers start: 20 outliers final: 18 residues processed: 81 average time/residue: 0.1452 time to fit residues: 16.2580 Evaluate side-chains 80 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 80 ASN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5571 Z= 0.324 Angle : 0.548 4.414 7548 Z= 0.299 Chirality : 0.048 0.148 936 Planarity : 0.003 0.029 960 Dihedral : 4.356 15.742 750 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.02 % Allowed : 18.57 % Favored : 78.41 % 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: -0.67 (0.32), residues: 711 helix: 0.57 (0.69), residues: 63 sheet: 0.11 (0.29), residues: 351 loop : -1.30 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.013 0.001 PHE H 231 TYR 0.017 0.001 TYR G 43 ARG 0.003 0.001 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: G 188 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7586 (t70) outliers start: 19 outliers final: 18 residues processed: 78 average time/residue: 0.1451 time to fit residues: 15.6630 Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5571 Z= 0.166 Angle : 0.461 4.210 7548 Z= 0.256 Chirality : 0.046 0.134 936 Planarity : 0.003 0.030 960 Dihedral : 3.968 14.849 750 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 18.89 % Favored : 77.78 % 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: -0.37 (0.31), residues: 711 helix: 0.73 (0.69), residues: 63 sheet: 0.66 (0.30), residues: 306 loop : -1.32 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 118 PHE 0.009 0.001 PHE H 231 TYR 0.013 0.001 TYR H 95 ARG 0.001 0.000 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: G 188 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7576 (t70) outliers start: 21 outliers final: 18 residues processed: 77 average time/residue: 0.1489 time to fit residues: 15.8863 Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 16 GLN I 80 ASN ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5571 Z= 0.339 Angle : 0.557 4.398 7548 Z= 0.304 Chirality : 0.048 0.149 936 Planarity : 0.003 0.029 960 Dihedral : 4.384 15.383 750 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.17 % Allowed : 19.68 % Favored : 77.14 % 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: -0.70 (0.32), residues: 711 helix: 0.48 (0.68), residues: 63 sheet: 0.12 (0.29), residues: 351 loop : -1.34 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.012 0.001 PHE H 231 TYR 0.018 0.002 TYR G 43 ARG 0.003 0.000 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: G 164 ASP cc_start: 0.7755 (p0) cc_final: 0.7356 (p0) REVERT: G 188 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7590 (t0) outliers start: 20 outliers final: 18 residues processed: 81 average time/residue: 0.1480 time to fit residues: 16.5367 Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 8 optimal weight: 9.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5571 Z= 0.114 Angle : 0.431 4.473 7548 Z= 0.239 Chirality : 0.045 0.132 936 Planarity : 0.003 0.031 960 Dihedral : 3.716 13.494 750 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.54 % Allowed : 20.48 % Favored : 76.98 % 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: -0.26 (0.32), residues: 711 helix: 0.83 (0.69), residues: 63 sheet: 0.74 (0.30), residues: 306 loop : -1.26 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.008 0.001 PHE H 231 TYR 0.008 0.001 TYR G 43 ARG 0.001 0.000 ARG I 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: H 45 GLU cc_start: 0.7853 (tt0) cc_final: 0.7622 (tt0) REVERT: G 164 ASP cc_start: 0.7490 (p0) cc_final: 0.7105 (p0) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.1624 time to fit residues: 17.8167 Evaluate side-chains 75 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** 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 = 0.3234 r_free = 0.3234 target = 0.115302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.103118 restraints weight = 7240.189| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.81 r_work: 0.2994 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5571 Z= 0.326 Angle : 0.549 4.523 7548 Z= 0.299 Chirality : 0.048 0.150 936 Planarity : 0.003 0.029 960 Dihedral : 4.262 15.115 750 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.54 % Allowed : 21.11 % Favored : 76.35 % 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: -0.48 (0.31), residues: 711 helix: 0.55 (0.68), residues: 63 sheet: 0.38 (0.30), residues: 321 loop : -1.19 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 118 PHE 0.013 0.001 PHE H 231 TYR 0.016 0.001 TYR G 43 ARG 0.002 0.000 ARG I 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.22 seconds wall clock time: 25 minutes 12.53 seconds (1512.53 seconds total)