Starting phenix.real_space_refine on Thu Dec 7 21:11:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpj_26057/12_2023/7tpj_26057.pdb" } resolution = 3.46 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 3071 2.51 5 N 816 2.21 5 O 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4758 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3053 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Time building chain proxies: 2.90, per 1000 atoms: 0.61 Number of scatterers: 4758 At special positions: 0 Unit cell: (77.453, 79.575, 106.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 839 8.00 N 816 7.00 C 3071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 1.83 Conformation dependent library (CDL) restraints added in 822.2 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 52.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.876A pdb=" N SER B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.544A pdb=" N LEU B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 75 removed outlier: 3.606A pdb=" N THR B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) Proline residue: B 61 - end of helix removed outlier: 5.368A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.521A pdb=" N ASP B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 89 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.629A pdb=" N LEU B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.255A pdb=" N TRP B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.964A pdb=" N ALA B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.524A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.653A pdb=" N VAL B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 214 through 230 removed outlier: 4.552A pdb=" N ALA B 220 " --> pdb=" O MET B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 4.058A pdb=" N VAL B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.668A pdb=" N TYR B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.951A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.984A pdb=" N ALA B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 352 removed outlier: 3.815A pdb=" N PHE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Proline residue: B 338 - end of helix removed outlier: 3.758A pdb=" N ALA B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.597A pdb=" N VAL B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 407 removed outlier: 3.821A pdb=" N LEU B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.744A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.997A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.672A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 51 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS H 99 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP H 116 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 101 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.672A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 51 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.626A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 753 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: 1.21 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1505 1.34 - 1.46: 1202 1.46 - 1.58: 2107 1.58 - 1.70: 1 1.70 - 1.81: 55 Bond restraints: 4870 Sorted by residual: bond pdb=" CB PRO B 238 " pdb=" CG PRO B 238 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.02e+01 bond pdb=" CG PRO B 238 " pdb=" CD PRO B 238 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.73e+00 bond pdb=" C VAL B 74 " pdb=" O VAL B 74 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.03e-02 9.43e+03 1.62e+00 bond pdb=" N PRO B 238 " pdb=" CA PRO B 238 " ideal model delta sigma weight residual 1.469 1.453 0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" C VAL B 337 " pdb=" N PRO B 338 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.38e+00 ... (remaining 4865 not shown) Histogram of bond angle deviations from ideal: 95.38 - 103.10: 50 103.10 - 110.82: 1675 110.82 - 118.54: 2104 118.54 - 126.26: 2703 126.26 - 133.98: 93 Bond angle restraints: 6625 Sorted by residual: angle pdb=" CA PRO B 238 " pdb=" N PRO B 238 " pdb=" CD PRO B 238 " ideal model delta sigma weight residual 112.00 98.38 13.62 1.40e+00 5.10e-01 9.46e+01 angle pdb=" N LEU B 62 " pdb=" CA LEU B 62 " pdb=" C LEU B 62 " ideal model delta sigma weight residual 114.75 107.20 7.55 1.26e+00 6.30e-01 3.59e+01 angle pdb=" N PRO B 238 " pdb=" CD PRO B 238 " pdb=" CG PRO B 238 " ideal model delta sigma weight residual 103.20 95.38 7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" N LEU B 217 " pdb=" CA LEU B 217 " pdb=" C LEU B 217 " ideal model delta sigma weight residual 113.55 108.86 4.69 1.26e+00 6.30e-01 1.38e+01 angle pdb=" N PRO B 238 " pdb=" CA PRO B 238 " pdb=" CB PRO B 238 " ideal model delta sigma weight residual 103.25 99.64 3.61 1.05e+00 9.07e-01 1.18e+01 ... (remaining 6620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 2547 16.70 - 33.39: 219 33.39 - 50.09: 61 50.09 - 66.78: 12 66.78 - 83.48: 7 Dihedral angle restraints: 2846 sinusoidal: 1059 harmonic: 1787 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 151.79 -58.79 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA PHE B 80 " pdb=" C PHE B 80 " pdb=" N HIS B 81 " pdb=" CA HIS B 81 " ideal model delta harmonic sigma weight residual 180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA MET B 48 " pdb=" C MET B 48 " pdb=" N GLY B 49 " pdb=" CA GLY B 49 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 458 0.031 - 0.062: 220 0.062 - 0.093: 61 0.093 - 0.124: 22 0.124 - 0.154: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA THR B 60 " pdb=" N THR B 60 " pdb=" C THR B 60 " pdb=" CB THR B 60 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" C PRO B 90 " pdb=" CB PRO B 90 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 760 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 237 " -0.094 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO B 238 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " -0.026 2.00e-02 2.50e+03 1.90e-02 9.05e+00 pdb=" CG TRP B 101 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 337 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO B 338 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.031 5.00e-02 4.00e+02 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 116 2.71 - 3.26: 4826 3.26 - 3.80: 7535 3.80 - 4.35: 9121 4.35 - 4.90: 15628 Nonbonded interactions: 37226 Sorted by model distance: nonbonded pdb=" O SER B 56 " pdb=" OG1 THR B 60 " model vdw 2.159 2.440 nonbonded pdb=" O ASN H 31 " pdb=" OG SER H 34 " model vdw 2.188 2.440 nonbonded pdb=" OG SER H 55 " pdb=" OG SER H 60 " model vdw 2.228 2.440 nonbonded pdb=" OG SER L 10 " pdb=" OE1 GLN L 101 " model vdw 2.290 2.440 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.291 2.440 ... (remaining 37221 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.560 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 0.160 4870 Z= 0.291 Angle : 0.700 13.618 6625 Z= 0.402 Chirality : 0.040 0.154 763 Planarity : 0.006 0.131 824 Dihedral : 14.421 83.478 1699 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.35), residues: 620 helix: 0.70 (0.31), residues: 298 sheet: 0.41 (0.58), residues: 91 loop : -1.02 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 101 HIS 0.004 0.001 HIS B 294 PHE 0.016 0.001 PHE H 113 TYR 0.019 0.002 TYR B 73 ARG 0.008 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1547 time to fit residues: 23.2639 Evaluate side-chains 99 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4870 Z= 0.238 Angle : 0.573 6.658 6625 Z= 0.299 Chirality : 0.041 0.156 763 Planarity : 0.005 0.063 824 Dihedral : 4.364 19.211 682 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.40 % Allowed : 11.42 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.35), residues: 620 helix: 0.91 (0.31), residues: 301 sheet: 0.61 (0.52), residues: 96 loop : -1.06 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 101 HIS 0.003 0.001 HIS B 294 PHE 0.014 0.001 PHE H 113 TYR 0.010 0.001 TYR L 56 ARG 0.006 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.498 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.1474 time to fit residues: 19.7240 Evaluate side-chains 101 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0471 time to fit residues: 1.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4870 Z= 0.195 Angle : 0.538 5.967 6625 Z= 0.278 Chirality : 0.039 0.149 763 Planarity : 0.004 0.052 824 Dihedral : 4.265 18.032 682 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.60 % Allowed : 13.03 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.36 (0.35), residues: 620 helix: 1.15 (0.31), residues: 301 sheet: 0.50 (0.53), residues: 94 loop : -1.08 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 101 HIS 0.003 0.001 HIS B 294 PHE 0.025 0.001 PHE B 69 TYR 0.014 0.001 TYR H 53 ARG 0.004 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.505 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.1621 time to fit residues: 21.9812 Evaluate side-chains 101 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0834 time to fit residues: 0.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4870 Z= 0.400 Angle : 0.689 7.282 6625 Z= 0.362 Chirality : 0.045 0.167 763 Planarity : 0.006 0.052 824 Dihedral : 4.942 21.389 682 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.80 % Allowed : 15.83 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.34), residues: 620 helix: 0.68 (0.31), residues: 299 sheet: 1.01 (0.55), residues: 87 loop : -1.35 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 101 HIS 0.006 0.002 HIS B 294 PHE 0.019 0.002 PHE B 69 TYR 0.018 0.002 TYR H 53 ARG 0.005 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.1552 time to fit residues: 21.9851 Evaluate side-chains 107 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0463 time to fit residues: 1.0930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4870 Z= 0.210 Angle : 0.566 7.336 6625 Z= 0.292 Chirality : 0.040 0.143 763 Planarity : 0.005 0.049 824 Dihedral : 4.569 19.370 682 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.40 % Allowed : 16.63 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.23 (0.34), residues: 620 helix: 1.01 (0.31), residues: 300 sheet: 1.09 (0.55), residues: 87 loop : -1.36 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.003 0.001 HIS B 294 PHE 0.016 0.001 PHE B 69 TYR 0.014 0.001 TYR H 53 ARG 0.005 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.477 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 104 average time/residue: 0.1571 time to fit residues: 21.3524 Evaluate side-chains 103 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0597 time to fit residues: 0.9529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4870 Z= 0.216 Angle : 0.573 7.456 6625 Z= 0.294 Chirality : 0.041 0.179 763 Planarity : 0.004 0.048 824 Dihedral : 4.477 18.708 682 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.40 % Allowed : 17.43 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.24 (0.34), residues: 620 helix: 1.07 (0.31), residues: 298 sheet: 1.14 (0.55), residues: 87 loop : -1.42 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 101 HIS 0.003 0.001 HIS B 294 PHE 0.014 0.001 PHE B 69 TYR 0.017 0.001 TYR B 275 ARG 0.004 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.460 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.1628 time to fit residues: 21.8070 Evaluate side-chains 100 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0571 time to fit residues: 1.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4870 Z= 0.184 Angle : 0.555 7.618 6625 Z= 0.284 Chirality : 0.040 0.170 763 Planarity : 0.004 0.047 824 Dihedral : 4.355 18.681 682 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.00 % Allowed : 19.24 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.40 (0.34), residues: 620 helix: 1.18 (0.31), residues: 298 sheet: 1.52 (0.59), residues: 77 loop : -1.34 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 PHE 0.012 0.001 PHE B 69 TYR 0.013 0.001 TYR B 275 ARG 0.003 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.576 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.1562 time to fit residues: 21.0742 Evaluate side-chains 100 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0653 time to fit residues: 1.0536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4870 Z= 0.213 Angle : 0.574 7.679 6625 Z= 0.293 Chirality : 0.040 0.172 763 Planarity : 0.004 0.048 824 Dihedral : 4.370 18.462 682 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.40 % Allowed : 19.84 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.47 (0.35), residues: 620 helix: 1.23 (0.31), residues: 298 sheet: 1.63 (0.60), residues: 77 loop : -1.30 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 PHE 0.012 0.001 PHE B 69 TYR 0.017 0.001 TYR B 275 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.526 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1591 time to fit residues: 19.8796 Evaluate side-chains 94 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0734 time to fit residues: 0.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4870 Z= 0.233 Angle : 0.596 7.764 6625 Z= 0.304 Chirality : 0.041 0.174 763 Planarity : 0.004 0.048 824 Dihedral : 4.455 19.861 682 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.00 % Allowed : 19.44 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.43 (0.35), residues: 620 helix: 1.19 (0.31), residues: 298 sheet: 1.72 (0.60), residues: 77 loop : -1.36 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 50 HIS 0.003 0.001 HIS B 294 PHE 0.012 0.001 PHE B 69 TYR 0.015 0.001 TYR H 53 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.526 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.1662 time to fit residues: 21.3447 Evaluate side-chains 96 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0638 time to fit residues: 0.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0000 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4870 Z= 0.190 Angle : 0.574 7.921 6625 Z= 0.290 Chirality : 0.039 0.163 763 Planarity : 0.004 0.047 824 Dihedral : 4.283 17.860 682 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.20 % Allowed : 20.44 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.63 (0.35), residues: 620 helix: 1.35 (0.31), residues: 298 sheet: 1.82 (0.60), residues: 77 loop : -1.26 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 PHE 0.011 0.001 PHE B 80 TYR 0.017 0.001 TYR B 275 ARG 0.003 0.000 ARG L 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1704 time to fit residues: 21.3823 Evaluate side-chains 94 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170316 restraints weight = 6547.737| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.13 r_work: 0.3829 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4870 Z= 0.195 Angle : 0.577 7.897 6625 Z= 0.292 Chirality : 0.039 0.166 763 Planarity : 0.004 0.048 824 Dihedral : 4.222 18.189 682 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.40 % Allowed : 20.84 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.35), residues: 620 helix: 1.40 (0.31), residues: 298 sheet: 1.91 (0.60), residues: 77 loop : -1.29 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.002 0.001 HIS B 294 PHE 0.011 0.001 PHE B 69 TYR 0.016 0.001 TYR B 275 ARG 0.002 0.000 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.93 seconds wall clock time: 24 minutes 26.27 seconds (1466.27 seconds total)