Starting phenix.real_space_refine on Mon Mar 11 03:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/03_2024/7r0c_14221_updated.pdb" } resolution = 4.73 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 39 5.16 5 C 4365 2.51 5 N 1158 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 40": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" 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: 6816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2810 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1750 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 4.17, per 1000 atoms: 0.61 Number of scatterers: 6816 At special positions: 0 Unit cell: (83.2, 99.84, 139.52, 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 P 6 15.00 O 1248 8.00 N 1158 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 6 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 222 " 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 10 sheets defined 26.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 34 through 68 Processing helix chain 'A' and resid 73 through 102 removed outlier: 3.924A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 110 through 141 removed outlier: 4.572A pdb=" N GLY A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 205 through 229 removed outlier: 5.019A pdb=" N ALA A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix removed outlier: 3.938A pdb=" N ILE A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.641A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 4.324A pdb=" N ASN A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 26 through 28 removed outlier: 7.216A pdb=" N ARG C 169 " --> pdb=" O PHE C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 163 through 168 removed outlier: 5.157A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'C' and resid 183 through 188 Processing sheet with id= F, first strand: chain 'C' and resid 343 through 349 removed outlier: 4.128A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 241 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN C 248 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= H, first strand: chain 'D' and resid 88 through 93 removed outlier: 5.897A pdb=" N GLN D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU D 49 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 129 through 133 Processing sheet with id= J, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.395A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 783 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: 1.86 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1179 1.32 - 1.45: 1797 1.45 - 1.57: 3926 1.57 - 1.69: 22 1.69 - 1.81: 52 Bond restraints: 6976 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 6971 not shown) Histogram of bond angle deviations from ideal: 95.08 - 102.88: 37 102.88 - 110.68: 2246 110.68 - 118.48: 3249 118.48 - 126.28: 3847 126.28 - 134.08: 121 Bond angle restraints: 9500 Sorted by residual: angle pdb=" N ILE A 74 " pdb=" CA ILE A 74 " pdb=" C ILE A 74 " ideal model delta sigma weight residual 110.42 101.79 8.63 9.60e-01 1.09e+00 8.08e+01 angle pdb=" N VAL A 76 " pdb=" CA VAL A 76 " pdb=" C VAL A 76 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 113.84 107.29 6.55 1.30e+00 5.92e-01 2.53e+01 angle pdb=" CA LYS D 202 " pdb=" CB LYS D 202 " pdb=" CG LYS D 202 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C LEU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 122.61 129.40 -6.79 1.56e+00 4.11e-01 1.89e+01 ... (remaining 9495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3812 16.88 - 33.77: 308 33.77 - 50.65: 54 50.65 - 67.54: 9 67.54 - 84.42: 8 Dihedral angle restraints: 4191 sinusoidal: 1628 harmonic: 2563 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS B 1 " pdb=" SG CYS B 1 " pdb=" SG CYS B 6 " pdb=" CB CYS B 6 " ideal model delta sinusoidal sigma weight residual 93.00 45.16 47.84 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ARG D 226 " pdb=" C ARG D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 4188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1040 0.108 - 0.215: 43 0.215 - 0.323: 1 0.323 - 0.430: 1 0.430 - 0.538: 1 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.97 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CA TRP A 71 " pdb=" N TRP A 71 " pdb=" C TRP A 71 " pdb=" CB TRP A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1083 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.015 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP A 99 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 94 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 95 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 359 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO C 360 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 193 2.66 - 3.22: 7065 3.22 - 3.78: 11210 3.78 - 4.34: 14385 4.34 - 4.90: 22458 Nonbonded interactions: 55311 Sorted by model distance: nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.100 2.520 nonbonded pdb=" OE1 GLN D 9 " pdb=" OG1 THR D 105 " model vdw 2.127 2.440 nonbonded pdb=" O GLN D 40 " pdb=" N LYS D 48 " model vdw 2.178 2.520 nonbonded pdb=" OG1 THR C 56 " pdb=" O ALA C 82 " model vdw 2.190 2.440 nonbonded pdb=" NZ LYS C 11 " pdb=" O ARG C 165 " model vdw 2.207 2.520 ... (remaining 55306 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.520 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: 2.560 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.005 0.110 6976 Z= 0.316 Angle : 0.909 12.782 9500 Z= 0.523 Chirality : 0.052 0.538 1086 Planarity : 0.005 0.060 1192 Dihedral : 13.187 84.422 2516 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.32 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.85 % 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: -0.89 (0.28), residues: 846 helix: -0.59 (0.32), residues: 209 sheet: -0.36 (0.34), residues: 245 loop : -0.59 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS C 159 PHE 0.023 0.002 PHE D 228 TYR 0.020 0.002 TYR A 128 ARG 0.008 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9158 (ppp) cc_final: 0.8925 (ppp) REVERT: A 288 PHE cc_start: 0.8903 (m-80) cc_final: 0.8337 (m-80) REVERT: C 75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5776 (m-10) REVERT: C 129 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt) REVERT: D 48 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8827 (tmtt) REVERT: D 49 LEU cc_start: 0.8528 (tp) cc_final: 0.8280 (tp) REVERT: D 50 LEU cc_start: 0.8422 (mt) cc_final: 0.7655 (mt) REVERT: D 74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8473 (m-80) REVERT: D 195 THR cc_start: 0.8680 (m) cc_final: 0.8416 (p) REVERT: D 209 MET cc_start: 0.6815 (mpp) cc_final: 0.6419 (mpp) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2005 time to fit residues: 34.6941 Evaluate side-chains 95 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6976 Z= 0.244 Angle : 0.653 7.887 9500 Z= 0.336 Chirality : 0.044 0.161 1086 Planarity : 0.005 0.058 1192 Dihedral : 6.589 80.640 965 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.75 (0.29), residues: 846 helix: -0.15 (0.33), residues: 206 sheet: -0.39 (0.33), residues: 247 loop : -0.61 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 99 HIS 0.005 0.002 HIS C 159 PHE 0.022 0.002 PHE D 228 TYR 0.012 0.002 TYR A 128 ARG 0.005 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9007 (ppp) cc_final: 0.8728 (ppp) REVERT: A 272 MET cc_start: 0.8460 (ppp) cc_final: 0.8188 (ppp) REVERT: A 288 PHE cc_start: 0.8988 (m-80) cc_final: 0.8456 (m-80) REVERT: C 10 LYS cc_start: 0.8082 (pttt) cc_final: 0.7413 (pttt) REVERT: C 75 PHE cc_start: 0.6719 (m-80) cc_final: 0.6000 (m-10) REVERT: C 223 ASN cc_start: 0.8232 (m-40) cc_final: 0.7770 (p0) REVERT: C 233 ILE cc_start: 0.9014 (mm) cc_final: 0.8798 (mm) REVERT: D 49 LEU cc_start: 0.8549 (tp) cc_final: 0.8184 (tt) REVERT: D 50 LEU cc_start: 0.8569 (mt) cc_final: 0.8237 (mt) REVERT: D 74 PHE cc_start: 0.9089 (m-80) cc_final: 0.8736 (m-80) REVERT: D 209 MET cc_start: 0.6989 (mpp) cc_final: 0.6439 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1859 time to fit residues: 31.5646 Evaluate side-chains 87 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6976 Z= 0.228 Angle : 0.634 7.172 9500 Z= 0.325 Chirality : 0.044 0.155 1086 Planarity : 0.005 0.059 1192 Dihedral : 6.530 80.750 965 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.69 (0.29), residues: 846 helix: -0.03 (0.34), residues: 206 sheet: -0.39 (0.34), residues: 247 loop : -0.59 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 99 HIS 0.005 0.001 HIS C 159 PHE 0.022 0.002 PHE D 228 TYR 0.020 0.002 TYR D 52 ARG 0.006 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7356 (mmp) cc_final: 0.7084 (mmp) REVERT: A 133 MET cc_start: 0.8979 (ppp) cc_final: 0.8708 (ppp) REVERT: A 288 PHE cc_start: 0.8894 (m-80) cc_final: 0.8516 (m-80) REVERT: C 29 ASP cc_start: 0.7995 (t0) cc_final: 0.7273 (t0) REVERT: C 75 PHE cc_start: 0.6774 (m-80) cc_final: 0.6038 (m-10) REVERT: C 223 ASN cc_start: 0.8169 (m-40) cc_final: 0.7766 (p0) REVERT: D 39 TYR cc_start: 0.7225 (m-80) cc_final: 0.6927 (m-10) REVERT: D 48 LYS cc_start: 0.9094 (tptt) cc_final: 0.8864 (tptt) REVERT: D 49 LEU cc_start: 0.8439 (tp) cc_final: 0.8066 (tt) REVERT: D 50 LEU cc_start: 0.8597 (mt) cc_final: 0.8232 (mt) REVERT: D 65 PHE cc_start: 0.8284 (m-10) cc_final: 0.7990 (m-80) REVERT: D 74 PHE cc_start: 0.9089 (m-80) cc_final: 0.8617 (m-80) REVERT: D 199 ASP cc_start: 0.8813 (t0) cc_final: 0.8611 (t0) REVERT: D 226 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8180 (ttp80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1984 time to fit residues: 33.0090 Evaluate side-chains 88 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.0030 chunk 22 optimal weight: 9.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6976 Z= 0.216 Angle : 0.625 6.936 9500 Z= 0.317 Chirality : 0.043 0.150 1086 Planarity : 0.005 0.058 1192 Dihedral : 6.462 80.655 965 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.64 (0.29), residues: 846 helix: 0.02 (0.34), residues: 206 sheet: -0.41 (0.33), residues: 247 loop : -0.52 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 38 HIS 0.004 0.001 HIS C 159 PHE 0.017 0.002 PHE D 228 TYR 0.012 0.002 TYR A 280 ARG 0.004 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7403 (mmp) cc_final: 0.7190 (mmp) REVERT: A 130 ILE cc_start: 0.9760 (mm) cc_final: 0.9549 (mm) REVERT: A 133 MET cc_start: 0.8997 (ppp) cc_final: 0.8727 (ppp) REVERT: A 272 MET cc_start: 0.8548 (ppp) cc_final: 0.8307 (ppp) REVERT: A 288 PHE cc_start: 0.8912 (m-80) cc_final: 0.8588 (m-80) REVERT: C 29 ASP cc_start: 0.8017 (t0) cc_final: 0.7328 (t0) REVERT: C 75 PHE cc_start: 0.6592 (m-80) cc_final: 0.5813 (m-10) REVERT: C 223 ASN cc_start: 0.8194 (m-40) cc_final: 0.7811 (p0) REVERT: C 232 LYS cc_start: 0.8873 (tppt) cc_final: 0.8445 (tppt) REVERT: D 39 TYR cc_start: 0.7312 (m-80) cc_final: 0.6855 (m-10) REVERT: D 48 LYS cc_start: 0.9103 (tptt) cc_final: 0.8856 (tptt) REVERT: D 50 LEU cc_start: 0.8503 (mt) cc_final: 0.8085 (mt) REVERT: D 65 PHE cc_start: 0.8201 (m-10) cc_final: 0.7961 (m-80) REVERT: D 74 PHE cc_start: 0.9011 (m-80) cc_final: 0.8641 (m-80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1853 time to fit residues: 31.1957 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6976 Z= 0.215 Angle : 0.624 6.747 9500 Z= 0.317 Chirality : 0.043 0.147 1086 Planarity : 0.005 0.058 1192 Dihedral : 6.405 80.604 965 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.64 (0.29), residues: 846 helix: 0.01 (0.34), residues: 206 sheet: -0.35 (0.33), residues: 244 loop : -0.56 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 99 HIS 0.004 0.001 HIS C 159 PHE 0.019 0.002 PHE D 228 TYR 0.010 0.001 TYR D 94 ARG 0.004 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7525 (mmp) cc_final: 0.7286 (mmp) REVERT: A 130 ILE cc_start: 0.9757 (mm) cc_final: 0.9556 (mm) REVERT: A 134 THR cc_start: 0.9416 (p) cc_final: 0.9114 (p) REVERT: A 288 PHE cc_start: 0.8932 (m-80) cc_final: 0.8567 (m-80) REVERT: C 29 ASP cc_start: 0.8025 (t0) cc_final: 0.7315 (t0) REVERT: C 75 PHE cc_start: 0.6620 (m-80) cc_final: 0.5836 (m-10) REVERT: C 223 ASN cc_start: 0.8181 (m-40) cc_final: 0.7815 (p0) REVERT: C 232 LYS cc_start: 0.8906 (tppt) cc_final: 0.8472 (tppt) REVERT: C 315 LEU cc_start: 0.9156 (mm) cc_final: 0.8945 (mm) REVERT: D 48 LYS cc_start: 0.9084 (tptt) cc_final: 0.8846 (tptt) REVERT: D 50 LEU cc_start: 0.8519 (mt) cc_final: 0.8179 (mt) REVERT: D 74 PHE cc_start: 0.8980 (m-80) cc_final: 0.8618 (m-80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1753 time to fit residues: 29.4515 Evaluate side-chains 92 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6976 Z= 0.222 Angle : 0.640 6.915 9500 Z= 0.324 Chirality : 0.044 0.150 1086 Planarity : 0.005 0.062 1192 Dihedral : 6.473 81.784 965 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.60 (0.29), residues: 846 helix: 0.09 (0.35), residues: 206 sheet: -0.38 (0.33), residues: 246 loop : -0.52 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 284 HIS 0.004 0.001 HIS C 159 PHE 0.017 0.002 PHE D 74 TYR 0.010 0.001 TYR C 173 ARG 0.004 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7638 (mmp) cc_final: 0.7433 (mmp) REVERT: A 133 MET cc_start: 0.9000 (ppp) cc_final: 0.8743 (ppp) REVERT: A 272 MET cc_start: 0.8587 (ppp) cc_final: 0.8366 (ppp) REVERT: A 288 PHE cc_start: 0.8956 (m-80) cc_final: 0.8535 (m-80) REVERT: C 29 ASP cc_start: 0.8016 (t0) cc_final: 0.7332 (t0) REVERT: C 75 PHE cc_start: 0.6800 (m-80) cc_final: 0.6108 (m-10) REVERT: C 166 LEU cc_start: 0.7826 (tt) cc_final: 0.7417 (tp) REVERT: C 223 ASN cc_start: 0.8192 (m-40) cc_final: 0.7849 (p0) REVERT: C 232 LYS cc_start: 0.8851 (tppt) cc_final: 0.8384 (tppt) REVERT: C 315 LEU cc_start: 0.9154 (mm) cc_final: 0.8932 (mm) REVERT: D 48 LYS cc_start: 0.9048 (tptt) cc_final: 0.8794 (tptt) REVERT: D 50 LEU cc_start: 0.8587 (mt) cc_final: 0.8101 (mt) REVERT: D 65 PHE cc_start: 0.7639 (m-80) cc_final: 0.7358 (m-80) REVERT: D 74 PHE cc_start: 0.9004 (m-80) cc_final: 0.8678 (m-80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1741 time to fit residues: 28.8324 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 119 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6976 Z= 0.241 Angle : 0.658 7.098 9500 Z= 0.335 Chirality : 0.044 0.160 1086 Planarity : 0.005 0.060 1192 Dihedral : 6.507 81.444 965 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.65 (0.29), residues: 846 helix: 0.06 (0.34), residues: 206 sheet: -0.47 (0.33), residues: 245 loop : -0.53 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 284 HIS 0.004 0.001 HIS C 30 PHE 0.019 0.002 PHE C 27 TYR 0.012 0.002 TYR C 173 ARG 0.005 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9045 (ppp) cc_final: 0.8776 (ppp) REVERT: A 134 THR cc_start: 0.9399 (p) cc_final: 0.9148 (p) REVERT: A 272 MET cc_start: 0.8667 (ppp) cc_final: 0.8426 (ppp) REVERT: A 288 PHE cc_start: 0.8967 (m-80) cc_final: 0.8519 (m-80) REVERT: C 29 ASP cc_start: 0.8051 (t0) cc_final: 0.7379 (t0) REVERT: C 75 PHE cc_start: 0.6835 (m-80) cc_final: 0.6140 (m-10) REVERT: C 223 ASN cc_start: 0.8213 (m-40) cc_final: 0.7855 (p0) REVERT: C 232 LYS cc_start: 0.8922 (tppt) cc_final: 0.8498 (tppt) REVERT: C 315 LEU cc_start: 0.9172 (mm) cc_final: 0.8939 (mm) REVERT: D 48 LYS cc_start: 0.9096 (tptt) cc_final: 0.8866 (tptt) REVERT: D 50 LEU cc_start: 0.8596 (mt) cc_final: 0.8193 (mt) REVERT: D 65 PHE cc_start: 0.7622 (m-80) cc_final: 0.7349 (m-80) REVERT: D 74 PHE cc_start: 0.8984 (m-80) cc_final: 0.8675 (m-80) REVERT: D 90 TYR cc_start: 0.7832 (m-10) cc_final: 0.7334 (m-80) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1780 time to fit residues: 29.2562 Evaluate side-chains 91 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 0.0470 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6976 Z= 0.176 Angle : 0.635 7.958 9500 Z= 0.314 Chirality : 0.044 0.155 1086 Planarity : 0.005 0.060 1192 Dihedral : 6.316 79.661 965 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.54 (0.29), residues: 846 helix: 0.04 (0.34), residues: 207 sheet: -0.26 (0.33), residues: 245 loop : -0.51 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 99 HIS 0.004 0.001 HIS C 159 PHE 0.017 0.002 PHE A 307 TYR 0.019 0.001 TYR D 52 ARG 0.004 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9081 (ppp) cc_final: 0.8704 (ppp) REVERT: A 272 MET cc_start: 0.8639 (ppp) cc_final: 0.8410 (ppp) REVERT: A 288 PHE cc_start: 0.9000 (m-80) cc_final: 0.8735 (m-80) REVERT: C 29 ASP cc_start: 0.7930 (t0) cc_final: 0.7295 (t0) REVERT: C 166 LEU cc_start: 0.7913 (tt) cc_final: 0.7607 (tp) REVERT: C 223 ASN cc_start: 0.8131 (m-40) cc_final: 0.7772 (p0) REVERT: C 232 LYS cc_start: 0.8877 (tppt) cc_final: 0.8415 (tppt) REVERT: D 48 LYS cc_start: 0.9037 (tptt) cc_final: 0.8779 (tptt) REVERT: D 50 LEU cc_start: 0.8599 (mt) cc_final: 0.8061 (mt) REVERT: D 65 PHE cc_start: 0.7619 (m-80) cc_final: 0.7319 (m-80) REVERT: D 74 PHE cc_start: 0.8941 (m-80) cc_final: 0.8649 (m-80) REVERT: D 90 TYR cc_start: 0.7698 (m-10) cc_final: 0.7191 (m-80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1870 time to fit residues: 30.6706 Evaluate side-chains 91 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6976 Z= 0.184 Angle : 0.637 7.923 9500 Z= 0.317 Chirality : 0.044 0.154 1086 Planarity : 0.005 0.060 1192 Dihedral : 6.234 79.405 965 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.29), residues: 846 helix: 0.19 (0.34), residues: 206 sheet: -0.48 (0.33), residues: 249 loop : -0.44 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 99 HIS 0.004 0.001 HIS C 159 PHE 0.015 0.002 PHE D 228 TYR 0.011 0.001 TYR C 173 ARG 0.004 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9748 (mm) cc_final: 0.9538 (mm) REVERT: A 133 MET cc_start: 0.9016 (ppp) cc_final: 0.8641 (ppp) REVERT: A 166 PHE cc_start: 0.7505 (t80) cc_final: 0.7297 (t80) REVERT: A 272 MET cc_start: 0.8566 (ppp) cc_final: 0.8352 (ppp) REVERT: A 288 PHE cc_start: 0.9012 (m-80) cc_final: 0.8723 (m-80) REVERT: C 75 PHE cc_start: 0.6758 (m-80) cc_final: 0.5975 (m-10) REVERT: C 166 LEU cc_start: 0.7876 (tt) cc_final: 0.7546 (tp) REVERT: C 223 ASN cc_start: 0.8146 (m-40) cc_final: 0.7802 (p0) REVERT: C 232 LYS cc_start: 0.8882 (tppt) cc_final: 0.8429 (tppt) REVERT: D 48 LYS cc_start: 0.8962 (tptt) cc_final: 0.8735 (tptt) REVERT: D 50 LEU cc_start: 0.8495 (mt) cc_final: 0.8008 (mt) REVERT: D 65 PHE cc_start: 0.7653 (m-80) cc_final: 0.7370 (m-80) REVERT: D 74 PHE cc_start: 0.8929 (m-80) cc_final: 0.8623 (m-80) REVERT: D 90 TYR cc_start: 0.7651 (m-10) cc_final: 0.7165 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1950 time to fit residues: 30.7434 Evaluate side-chains 91 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6976 Z= 0.167 Angle : 0.627 7.675 9500 Z= 0.309 Chirality : 0.044 0.153 1086 Planarity : 0.005 0.059 1192 Dihedral : 6.099 78.328 965 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.29), residues: 846 helix: 0.32 (0.35), residues: 206 sheet: -0.41 (0.33), residues: 249 loop : -0.46 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 99 HIS 0.003 0.001 HIS C 159 PHE 0.014 0.001 PHE D 228 TYR 0.018 0.001 TYR A 280 ARG 0.004 0.000 ARG D 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.5931 (t80) cc_final: 0.5720 (t80) REVERT: A 130 ILE cc_start: 0.9739 (mm) cc_final: 0.9531 (mm) REVERT: A 133 MET cc_start: 0.9095 (ppp) cc_final: 0.8812 (ppp) REVERT: A 212 MET cc_start: 0.8934 (ppp) cc_final: 0.8690 (ppp) REVERT: A 272 MET cc_start: 0.8563 (ppp) cc_final: 0.8342 (ppp) REVERT: A 288 PHE cc_start: 0.9021 (m-80) cc_final: 0.8710 (m-80) REVERT: C 75 PHE cc_start: 0.6609 (m-80) cc_final: 0.5859 (m-10) REVERT: C 166 LEU cc_start: 0.7864 (tt) cc_final: 0.7547 (tp) REVERT: C 223 ASN cc_start: 0.8126 (m-40) cc_final: 0.7791 (p0) REVERT: C 232 LYS cc_start: 0.8927 (tppt) cc_final: 0.8490 (tppt) REVERT: D 48 LYS cc_start: 0.9067 (tptt) cc_final: 0.8831 (tptt) REVERT: D 50 LEU cc_start: 0.8502 (mt) cc_final: 0.8010 (mt) REVERT: D 65 PHE cc_start: 0.7656 (m-80) cc_final: 0.7380 (m-80) REVERT: D 90 TYR cc_start: 0.7690 (m-10) cc_final: 0.7090 (m-80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1839 time to fit residues: 30.1404 Evaluate side-chains 92 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090172 restraints weight = 28441.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093194 restraints weight = 17853.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.095269 restraints weight = 12794.341| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6976 Z= 0.155 Angle : 0.615 7.463 9500 Z= 0.302 Chirality : 0.044 0.150 1086 Planarity : 0.005 0.059 1192 Dihedral : 5.903 76.746 965 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.42 (0.29), residues: 846 helix: 0.36 (0.35), residues: 206 sheet: -0.31 (0.33), residues: 249 loop : -0.47 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 99 HIS 0.003 0.001 HIS A 75 PHE 0.022 0.001 PHE A 166 TYR 0.013 0.001 TYR D 94 ARG 0.004 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.04 seconds wall clock time: 30 minutes 38.00 seconds (1838.00 seconds total)