Starting phenix.real_space_refine on Sat Mar 16 02:47:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk7_25175/03_2024/7sk7_25175_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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 S 39 5.16 5 C 4415 2.51 5 N 1114 2.21 5 O 1237 1.98 5 H 6650 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13455 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 4398 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 267, 4398 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 3 bond proxies already assigned to first conformer: 4444 Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1050 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "C" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3211 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "D" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3179 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 2 Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1537 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 4 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'CLR': 1, 'GJ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 121 " occ=0.50 ... (29 atoms not shown) pdb=" HE1BHIS A 121 " occ=0.50 Time building chain proxies: 8.20, per 1000 atoms: 0.61 Number of scatterers: 13455 At special positions: 0 Unit cell: (83.16, 88.56, 142.56, 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 39 16.00 O 1237 8.00 N 1114 7.00 C 4415 6.00 H 6650 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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: 9.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 14 sheets defined 27.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 3.871A pdb=" N PHE A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.833A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.502A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 181 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 206 through 220 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 251 through 279 removed outlier: 4.057A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 287 through 316 removed outlier: 4.665A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.618A pdb=" N LYS C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 128' Processing helix chain 'C' and resid 184 through 189 removed outlier: 4.531A pdb=" N LYS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 removed outlier: 4.009A pdb=" N ARG A 197 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 26 through 31 Processing sheet with id= C, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= D, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.136A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 34 through 39 Processing sheet with id= F, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.744A pdb=" N VAL C 134 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 146 through 151 Processing sheet with id= H, first strand: chain 'D' and resid 7 through 10 removed outlier: 3.960A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 20 through 23 Processing sheet with id= J, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.525A pdb=" N TYR D 97 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 95 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.560A pdb=" N LYS D 158 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.696A pdb=" N THR D 166 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.534A pdb=" N CYS K 22 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 95 through 98 removed outlier: 6.051A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 764 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: 4.39 Time building geometry restraints manager: 10.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6639 1.03 - 1.23: 42 1.23 - 1.42: 2993 1.42 - 1.62: 3912 1.62 - 1.82: 51 Bond restraints: 13637 Sorted by residual: bond pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.446 1.521 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C14 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.416 1.473 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C20 CLR A 402 " pdb=" C22 CLR A 402 " ideal model delta sigma weight residual 1.535 1.592 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.495 1.550 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C14 CLR A 402 " pdb=" C15 CLR A 402 " ideal model delta sigma weight residual 1.523 1.578 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 13632 not shown) Histogram of bond angle deviations from ideal: 89.77 - 98.61: 3 98.61 - 107.45: 491 107.45 - 116.29: 16850 116.29 - 125.14: 6845 125.14 - 133.98: 324 Bond angle restraints: 24513 Sorted by residual: angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 103.44 8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" C08 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 108.48 116.45 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" C04 GJ9 A 401 " pdb=" N05 GJ9 A 401 " pdb=" C06 GJ9 A 401 " ideal model delta sigma weight residual 118.70 111.43 7.27 3.00e+00 1.11e-01 5.87e+00 angle pdb=" CA PRO C 41 " pdb=" N PRO C 41 " pdb=" CD PRO C 41 " ideal model delta sigma weight residual 112.00 108.80 3.20 1.40e+00 5.10e-01 5.22e+00 angle pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " pdb=" C25 CLR A 402 " ideal model delta sigma weight residual 115.14 108.51 6.63 3.00e+00 1.11e-01 4.88e+00 ... (remaining 24508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5977 17.70 - 35.41: 487 35.41 - 53.11: 122 53.11 - 70.82: 17 70.82 - 88.52: 10 Dihedral angle restraints: 6613 sinusoidal: 3512 harmonic: 3101 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -124.77 38.77 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CB CYS B 9 " pdb=" SG CYS B 9 " pdb=" SG CYS B 34 " pdb=" CB CYS B 34 " ideal model delta sinusoidal sigma weight residual -86.00 -59.31 -26.69 1 1.00e+01 1.00e-02 1.02e+01 dihedral pdb=" CA SER C 51 " pdb=" C SER C 51 " pdb=" N ALA C 52 " pdb=" CA ALA C 52 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 991 0.079 - 0.157: 83 0.157 - 0.236: 2 0.236 - 0.314: 1 0.314 - 0.393: 2 Chirality restraints: 1079 Sorted by residual: chirality pdb=" N10 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C34 GJ9 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.62 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C13 CLR A 402 " pdb=" C12 CLR A 402 " pdb=" C14 CLR A 402 " pdb=" C17 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.93 -3.32 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C20 CLR A 402 " pdb=" C17 CLR A 402 " pdb=" C21 CLR A 402 " pdb=" C22 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.59 2.83 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1076 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 41 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 59 " -0.036 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO C 60 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 97 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 98 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.027 5.00e-02 4.00e+02 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1087 2.22 - 2.81: 27976 2.81 - 3.41: 34054 3.41 - 4.00: 47314 4.00 - 4.60: 71594 Nonbonded interactions: 182025 Sorted by model distance: nonbonded pdb=" H VAL C 34 " pdb=" O SER C 51 " model vdw 1.623 1.850 nonbonded pdb=" OE1 GLN C 101 " pdb=" H GLN C 101 " model vdw 1.687 1.850 nonbonded pdb=" O ASP C 83 " pdb=" HH TYR C 87 " model vdw 1.698 1.850 nonbonded pdb=" OD1 ASN K 84 " pdb=" H SER K 85 " model vdw 1.702 1.850 nonbonded pdb=" O HIS C 190 " pdb=" HE ARG C 212 " model vdw 1.723 1.850 ... (remaining 182020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 2.070 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: 0.210 Extract box with map and model: 6.650 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 46.150 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.075 6987 Z= 0.307 Angle : 0.571 8.509 9518 Z= 0.273 Chirality : 0.045 0.393 1079 Planarity : 0.004 0.083 1167 Dihedral : 14.161 88.521 2527 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.04 (0.30), residues: 827 helix: 1.11 (0.35), residues: 228 sheet: -0.02 (0.34), residues: 255 loop : -0.71 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 PHE 0.009 0.001 PHE B 14 TYR 0.015 0.001 TYR D 53 ARG 0.002 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4247 time to fit residues: 76.4787 Evaluate side-chains 118 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6987 Z= 0.195 Angle : 0.514 4.620 9518 Z= 0.269 Chirality : 0.041 0.138 1079 Planarity : 0.004 0.050 1167 Dihedral : 5.841 57.338 1034 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.80 % Allowed : 5.97 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.04 (0.30), residues: 827 helix: 1.25 (0.35), residues: 228 sheet: 0.08 (0.33), residues: 257 loop : -0.78 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 208 HIS 0.003 0.001 HIS A 307 PHE 0.011 0.001 PHE A 294 TYR 0.019 0.001 TYR D 53 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.7730 (ptp-110) cc_final: 0.7295 (ptm-80) REVERT: C 186 ASP cc_start: 0.7280 (m-30) cc_final: 0.7030 (m-30) outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.4269 time to fit residues: 70.4136 Evaluate side-chains 121 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain K residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6987 Z= 0.183 Angle : 0.486 4.732 9518 Z= 0.252 Chirality : 0.041 0.136 1079 Planarity : 0.004 0.046 1167 Dihedral : 5.602 55.135 1034 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.80 % Allowed : 6.63 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.09 (0.30), residues: 827 helix: 1.39 (0.35), residues: 227 sheet: 0.09 (0.33), residues: 260 loop : -0.82 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 208 HIS 0.003 0.001 HIS A 307 PHE 0.010 0.001 PHE A 294 TYR 0.016 0.001 TYR D 53 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 124 average time/residue: 0.4136 time to fit residues: 67.4060 Evaluate side-chains 119 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6987 Z= 0.222 Angle : 0.494 4.738 9518 Z= 0.257 Chirality : 0.041 0.136 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.666 54.522 1034 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.33 % Allowed : 7.29 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.10 (0.30), residues: 827 helix: 1.37 (0.35), residues: 227 sheet: 0.12 (0.33), residues: 255 loop : -0.79 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 294 TYR 0.015 0.001 TYR D 53 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.3908 time to fit residues: 65.3403 Evaluate side-chains 121 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6987 Z= 0.222 Angle : 0.500 4.754 9518 Z= 0.258 Chirality : 0.041 0.136 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.698 55.108 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.06 % Allowed : 8.62 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.30), residues: 827 helix: 1.40 (0.35), residues: 228 sheet: 0.11 (0.33), residues: 255 loop : -0.80 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 118 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 294 TYR 0.013 0.001 TYR D 53 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.3797 time to fit residues: 61.1147 Evaluate side-chains 118 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6987 Z= 0.285 Angle : 0.528 5.013 9518 Z= 0.274 Chirality : 0.041 0.139 1079 Planarity : 0.004 0.044 1167 Dihedral : 5.896 57.951 1034 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 9.42 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.01 (0.30), residues: 827 helix: 1.30 (0.35), residues: 227 sheet: 0.18 (0.33), residues: 253 loop : -0.95 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 118 HIS 0.005 0.001 HIS A 298 PHE 0.012 0.001 PHE A 294 TYR 0.015 0.001 TYR D 58 ARG 0.003 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 119 average time/residue: 0.4217 time to fit residues: 66.8392 Evaluate side-chains 121 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6987 Z= 0.241 Angle : 0.514 4.880 9518 Z= 0.266 Chirality : 0.041 0.137 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.858 58.680 1034 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.59 % Allowed : 9.81 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.06 (0.30), residues: 827 helix: 1.34 (0.35), residues: 228 sheet: 0.17 (0.33), residues: 248 loop : -0.88 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 294 TYR 0.012 0.001 TYR C 87 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.4097 time to fit residues: 66.2909 Evaluate side-chains 120 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6987 Z= 0.201 Angle : 0.496 4.664 9518 Z= 0.256 Chirality : 0.041 0.136 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.731 58.187 1034 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.93 % Allowed : 11.27 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.15 (0.30), residues: 827 helix: 1.45 (0.35), residues: 228 sheet: 0.14 (0.33), residues: 252 loop : -0.79 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 208 HIS 0.003 0.001 HIS A 307 PHE 0.010 0.001 PHE A 294 TYR 0.011 0.001 TYR C 87 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6992 (mm-30) outliers start: 7 outliers final: 7 residues processed: 122 average time/residue: 0.4167 time to fit residues: 67.3296 Evaluate side-chains 120 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6987 Z= 0.241 Angle : 0.508 4.872 9518 Z= 0.263 Chirality : 0.041 0.138 1079 Planarity : 0.004 0.044 1167 Dihedral : 5.790 59.235 1034 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 11.14 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.12 (0.30), residues: 827 helix: 1.39 (0.35), residues: 228 sheet: 0.21 (0.33), residues: 248 loop : -0.84 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 169 HIS 0.004 0.001 HIS A 298 PHE 0.011 0.001 PHE A 294 TYR 0.012 0.001 TYR C 87 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7013 (mm-30) outliers start: 10 outliers final: 9 residues processed: 122 average time/residue: 0.4021 time to fit residues: 64.8002 Evaluate side-chains 124 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6987 Z= 0.198 Angle : 0.500 4.725 9518 Z= 0.257 Chirality : 0.041 0.137 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.718 59.283 1034 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.80 % Allowed : 12.07 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.17 (0.30), residues: 827 helix: 1.46 (0.35), residues: 228 sheet: 0.17 (0.33), residues: 252 loop : -0.78 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 169 HIS 0.003 0.001 HIS A 307 PHE 0.010 0.001 PHE A 294 TYR 0.015 0.001 TYR A 82 ARG 0.002 0.000 ARG C 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6982 (mm-30) outliers start: 6 outliers final: 6 residues processed: 118 average time/residue: 0.4142 time to fit residues: 64.8512 Evaluate side-chains 120 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116590 restraints weight = 33973.669| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.37 r_work: 0.3248 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6987 Z= 0.221 Angle : 0.505 4.760 9518 Z= 0.260 Chirality : 0.041 0.137 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.740 60.000 1034 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.59 % Allowed : 11.54 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.12 (0.30), residues: 827 helix: 1.41 (0.35), residues: 228 sheet: 0.16 (0.33), residues: 252 loop : -0.83 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 169 HIS 0.004 0.001 HIS A 298 PHE 0.010 0.001 PHE A 294 TYR 0.012 0.001 TYR C 87 ARG 0.002 0.000 ARG C 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3768.57 seconds wall clock time: 67 minutes 0.93 seconds (4020.93 seconds total)