Starting phenix.real_space_refine on Sun Mar 10 19:14:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/03_2024/5msh_3565.pdb" } resolution = 4.25 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= 0.003 sd= 0.022 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 31 5.16 5 C 2732 2.51 5 N 719 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1422 Classifications: {'peptide': 182} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2865 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 14, 'TRANS': 354} Time building chain proxies: 2.69, per 1000 atoms: 0.63 Number of scatterers: 4287 At special positions: 0 Unit cell: (92.4, 74.8, 99, 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 31 16.00 O 805 8.00 N 719 7.00 C 2732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 965.8 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 12.9% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA A 63 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 174 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.654A pdb=" N ARG A 106 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32 removed outlier: 5.989A pdb=" N LYS B 24 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 172 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.330A pdb=" N VAL B 150 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 44 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET B 148 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS B 87 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 111 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 174 hydrogen bonds defined for protein. 417 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: 1.30 Time building geometry restraints manager: 1.87 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: 1083 1.32 - 1.45: 1049 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4398 Sorted by residual: bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.466 1.406 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 1.467 1.418 0.048 1.17e-02 7.31e+03 1.72e+01 bond pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta sigma weight residual 1.466 1.420 0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta sigma weight residual 1.467 1.421 0.046 1.21e-02 6.83e+03 1.47e+01 bond pdb=" N PRO B 324 " pdb=" CA PRO B 324 " ideal model delta sigma weight residual 1.466 1.424 0.042 1.19e-02 7.06e+03 1.22e+01 ... (remaining 4393 not shown) Histogram of bond angle deviations from ideal: 97.76 - 104.98: 109 104.98 - 112.21: 2100 112.21 - 119.43: 1514 119.43 - 126.66: 2211 126.66 - 133.89: 56 Bond angle restraints: 5990 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.80 113.22 7.58 1.11e+00 8.12e-01 4.67e+01 angle pdb=" C GLY A 126 " pdb=" N PRO A 127 " pdb=" CA PRO A 127 " ideal model delta sigma weight residual 119.64 125.81 -6.17 1.01e+00 9.80e-01 3.73e+01 angle pdb=" C GLY A 1 " pdb=" N PRO A 2 " pdb=" CA PRO A 2 " ideal model delta sigma weight residual 119.56 125.71 -6.15 1.01e+00 9.80e-01 3.71e+01 angle pdb=" C GLU B 178 " pdb=" N PRO B 179 " pdb=" CA PRO B 179 " ideal model delta sigma weight residual 120.31 126.08 -5.77 9.80e-01 1.04e+00 3.46e+01 angle pdb=" C ASN A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.84 127.08 -7.24 1.25e+00 6.40e-01 3.35e+01 ... (remaining 5985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2515 17.09 - 34.18: 44 34.18 - 51.27: 11 51.27 - 68.36: 7 68.36 - 85.44: 6 Dihedral angle restraints: 2583 sinusoidal: 998 harmonic: 1585 Sorted by residual: dihedral pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta harmonic sigma weight residual 0.00 36.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" C HIS B 66 " pdb=" N HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual 122.80 131.11 -8.31 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 505 0.083 - 0.166: 141 0.166 - 0.249: 17 0.249 - 0.333: 2 0.333 - 0.416: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CA HIS B 66 " pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CB HIS B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA MET B 231 " pdb=" N MET B 231 " pdb=" C MET B 231 " pdb=" CB MET B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN B 233 " pdb=" N ASN B 233 " pdb=" C ASN B 233 " pdb=" CB ASN B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 663 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " -0.061 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ARG A 77 " 0.216 2.00e-02 2.50e+03 pdb=" O ARG A 77 " -0.080 2.00e-02 2.50e+03 pdb=" N GLY A 78 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 128 " 0.052 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 129 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " 0.036 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " 0.017 2.00e-02 2.50e+03 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1481 2.84 - 3.35: 3794 3.35 - 3.87: 7265 3.87 - 4.38: 8569 4.38 - 4.90: 14240 Nonbonded interactions: 35349 Sorted by model distance: nonbonded pdb=" O ASN B 128 " pdb=" OD1 ASN B 128 " model vdw 2.323 3.040 nonbonded pdb=" N GLU B 279 " pdb=" OE1 GLU B 279 " model vdw 2.326 2.520 nonbonded pdb=" OG SER B 366 " pdb=" N ARG B 367 " model vdw 2.420 2.520 nonbonded pdb=" O PHE A 133 " pdb=" CD1 PHE A 133 " model vdw 2.429 3.340 nonbonded pdb=" N GLU A 101 " pdb=" OE1 GLU A 101 " model vdw 2.467 2.520 ... (remaining 35344 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=1.00 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: 2.540 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: 11.580 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0197 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 : 0.014 0.059 4398 Z= 0.942 Angle : 1.562 9.020 5990 Z= 1.032 Chirality : 0.074 0.416 666 Planarity : 0.009 0.125 772 Dihedral : 9.556 85.444 1561 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 1.47 % Allowed : 6.06 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.93 (0.34), residues: 545 helix: -2.30 (0.58), residues: 57 sheet: 0.82 (0.38), residues: 181 loop : -1.20 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP A 47 HIS 0.003 0.001 HIS B 247 PHE 0.026 0.004 PHE B 202 TYR 0.031 0.005 TYR B 100 ARG 0.004 0.001 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.6148 (tttt) cc_final: 0.4973 (mtmm) REVERT: A 89 GLN cc_start: 0.3743 (mt0) cc_final: 0.3304 (pt0) REVERT: B 24 LYS cc_start: -0.1135 (mttm) cc_final: -0.1570 (mttt) REVERT: B 200 LEU cc_start: 0.3159 (mt) cc_final: 0.2814 (mp) REVERT: B 347 LYS cc_start: 0.5153 (ttpt) cc_final: 0.4869 (pttt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2499 time to fit residues: 19.5637 Evaluate side-chains 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0494 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4398 Z= 0.204 Angle : 0.672 6.305 5990 Z= 0.364 Chirality : 0.049 0.165 666 Planarity : 0.005 0.047 772 Dihedral : 5.326 29.831 587 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.44 (0.34), residues: 545 helix: -1.47 (0.68), residues: 51 sheet: 0.78 (0.39), residues: 176 loop : -0.71 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.006 0.002 HIS B 331 PHE 0.013 0.002 PHE A 32 TYR 0.010 0.001 TYR B 278 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 2 GLU cc_start: -0.0348 (mt-10) cc_final: -0.0630 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1880 time to fit residues: 11.7968 Evaluate side-chains 33 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0707 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4398 Z= 0.226 Angle : 0.667 8.254 5990 Z= 0.360 Chirality : 0.049 0.424 666 Planarity : 0.005 0.050 772 Dihedral : 5.355 24.508 587 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 0.42 % Allowed : 1.90 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.31 (0.34), residues: 545 helix: -1.44 (0.70), residues: 52 sheet: 0.72 (0.40), residues: 171 loop : -0.47 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.013 0.003 HIS A 50 PHE 0.015 0.002 PHE A 32 TYR 0.020 0.002 TYR B 241 ARG 0.005 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 2 GLU cc_start: -0.0388 (mt-10) cc_final: -0.0758 (tm-30) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1540 time to fit residues: 9.1826 Evaluate side-chains 34 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 40.0000 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 46 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN B 183 HIS ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1176 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 4398 Z= 0.430 Angle : 0.990 13.828 5990 Z= 0.540 Chirality : 0.060 0.358 666 Planarity : 0.008 0.068 772 Dihedral : 7.119 31.245 587 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 0.63 % Allowed : 2.53 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.33), residues: 545 helix: -2.02 (0.64), residues: 51 sheet: 0.04 (0.39), residues: 175 loop : -1.32 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 86 HIS 0.007 0.002 HIS A 50 PHE 0.068 0.004 PHE A 24 TYR 0.034 0.004 TYR A 93 ARG 0.008 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.0864 (OUTLIER) cc_final: -0.0411 (t0) REVERT: A 82 LYS cc_start: 0.6679 (tppt) cc_final: 0.5786 (ptpp) REVERT: A 148 CYS cc_start: 0.3568 (m) cc_final: 0.3264 (m) REVERT: B 199 LYS cc_start: -0.1099 (tttt) cc_final: -0.1657 (mttt) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1671 time to fit residues: 12.2355 Evaluate side-chains 44 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1160 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4398 Z= 0.263 Angle : 0.754 10.586 5990 Z= 0.404 Chirality : 0.049 0.243 666 Planarity : 0.006 0.069 772 Dihedral : 6.030 25.361 587 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.34), residues: 545 helix: -2.08 (0.63), residues: 58 sheet: -0.17 (0.38), residues: 191 loop : -1.24 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 47 HIS 0.004 0.001 HIS A 50 PHE 0.025 0.003 PHE A 24 TYR 0.025 0.002 TYR A 145 ARG 0.004 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.503 Fit side-chains REVERT: A 56 ILE cc_start: 0.2300 (mt) cc_final: 0.1884 (mt) REVERT: A 57 MET cc_start: 0.3618 (tpp) cc_final: 0.2352 (mmp) REVERT: A 163 MET cc_start: -0.0899 (tmm) cc_final: -0.3205 (mtp) REVERT: A 164 ARG cc_start: 0.0432 (tpm170) cc_final: 0.0114 (tpm170) REVERT: B 59 THR cc_start: 0.2889 (t) cc_final: 0.2606 (t) REVERT: B 199 LYS cc_start: -0.1064 (tttt) cc_final: -0.1584 (mttm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1815 time to fit residues: 10.8193 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 40.0000 chunk 52 optimal weight: 0.0370 chunk 43 optimal weight: 40.0000 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 50 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 overall best weight: 3.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 73 GLN B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1068 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4398 Z= 0.165 Angle : 0.603 6.299 5990 Z= 0.322 Chirality : 0.046 0.169 666 Planarity : 0.005 0.057 772 Dihedral : 5.225 18.758 587 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.35), residues: 545 helix: -1.99 (0.63), residues: 58 sheet: 0.00 (0.38), residues: 188 loop : -1.07 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.002 0.001 HIS B 66 PHE 0.011 0.002 PHE A 180 TYR 0.015 0.001 TYR A 145 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.2556 (mt) cc_final: 0.2334 (mt) REVERT: A 57 MET cc_start: 0.3347 (tpp) cc_final: 0.2088 (mmm) REVERT: A 163 MET cc_start: -0.1118 (tmm) cc_final: -0.3488 (mtp) REVERT: A 164 ARG cc_start: 0.0295 (tpm170) cc_final: 0.0044 (tpm170) REVERT: B 24 LYS cc_start: -0.2147 (mttm) cc_final: -0.2702 (pttt) REVERT: B 199 LYS cc_start: -0.1325 (tttt) cc_final: -0.1865 (mttm) REVERT: B 214 PRO cc_start: 0.2942 (Cg_exo) cc_final: 0.2457 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2096 time to fit residues: 12.1492 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 40.0000 overall best weight: 11.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1323 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4398 Z= 0.342 Angle : 0.834 15.443 5990 Z= 0.447 Chirality : 0.052 0.226 666 Planarity : 0.007 0.070 772 Dihedral : 6.458 30.454 587 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.26 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.34), residues: 545 helix: -1.60 (0.72), residues: 47 sheet: -0.29 (0.40), residues: 174 loop : -1.35 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 86 HIS 0.009 0.002 HIS A 50 PHE 0.032 0.003 PHE A 24 TYR 0.032 0.003 TYR A 93 ARG 0.007 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.2381 (mt) cc_final: 0.2049 (mt) REVERT: A 57 MET cc_start: 0.3804 (tpp) cc_final: 0.2678 (mmp) REVERT: A 163 MET cc_start: -0.1073 (tmm) cc_final: -0.3463 (mtp) REVERT: A 164 ARG cc_start: 0.0018 (tpm170) cc_final: -0.0303 (tpm170) REVERT: B 59 THR cc_start: 0.2861 (t) cc_final: 0.2633 (t) REVERT: B 199 LYS cc_start: -0.0849 (tttt) cc_final: -0.1396 (mttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1827 time to fit residues: 10.0472 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 50.0000 chunk 25 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1240 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4398 Z= 0.207 Angle : 0.671 10.728 5990 Z= 0.355 Chirality : 0.047 0.158 666 Planarity : 0.006 0.060 772 Dihedral : 5.692 22.790 587 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.34), residues: 545 helix: -1.36 (0.70), residues: 47 sheet: -0.29 (0.40), residues: 182 loop : -1.31 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 170 HIS 0.003 0.001 HIS A 50 PHE 0.022 0.002 PHE A 32 TYR 0.015 0.002 TYR B 325 ARG 0.004 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.2465 (mt) cc_final: 0.2045 (mt) REVERT: A 57 MET cc_start: 0.3564 (tpp) cc_final: 0.2493 (mmp) REVERT: A 163 MET cc_start: -0.0893 (tmm) cc_final: -0.3259 (mtp) REVERT: A 164 ARG cc_start: 0.0170 (tpm170) cc_final: -0.0123 (tpm170) REVERT: B 199 LYS cc_start: -0.0763 (tttt) cc_final: -0.1305 (mttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2118 time to fit residues: 11.2429 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1253 moved from start: 0.8300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4398 Z= 0.208 Angle : 0.660 9.571 5990 Z= 0.351 Chirality : 0.047 0.165 666 Planarity : 0.006 0.055 772 Dihedral : 5.499 22.103 587 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.34), residues: 545 helix: -1.24 (0.73), residues: 47 sheet: -0.18 (0.38), residues: 192 loop : -1.46 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.004 0.001 HIS A 50 PHE 0.026 0.002 PHE A 24 TYR 0.017 0.002 TYR A 93 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.465 Fit side-chains REVERT: A 56 ILE cc_start: 0.2557 (mt) cc_final: 0.2166 (mt) REVERT: A 57 MET cc_start: 0.4016 (tpp) cc_final: 0.2961 (mmp) REVERT: A 163 MET cc_start: -0.0928 (tmm) cc_final: -0.2975 (mtp) REVERT: A 164 ARG cc_start: 0.0096 (tpm170) cc_final: -0.0146 (tpm170) REVERT: A 177 MET cc_start: 0.0196 (mmm) cc_final: -0.0014 (mmm) REVERT: B 59 THR cc_start: 0.2822 (t) cc_final: 0.2595 (t) REVERT: B 97 ARG cc_start: 0.1981 (mmt-90) cc_final: 0.1454 (ttp80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1850 time to fit residues: 9.3750 Evaluate side-chains 34 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 40.0000 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1190 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4398 Z= 0.159 Angle : 0.600 8.633 5990 Z= 0.318 Chirality : 0.046 0.188 666 Planarity : 0.005 0.053 772 Dihedral : 5.034 17.722 587 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.35), residues: 545 helix: -0.57 (0.85), residues: 40 sheet: -0.15 (0.38), residues: 194 loop : -1.29 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.003 0.001 HIS A 50 PHE 0.015 0.002 PHE A 24 TYR 0.014 0.001 TYR A 145 ARG 0.003 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.490 Fit side-chains REVERT: A 56 ILE cc_start: 0.2592 (mt) cc_final: 0.2219 (mt) REVERT: A 57 MET cc_start: 0.3703 (tpp) cc_final: 0.2765 (mmp) REVERT: A 163 MET cc_start: -0.1085 (tmm) cc_final: -0.3055 (mtp) REVERT: A 164 ARG cc_start: 0.0096 (tpm170) cc_final: -0.0106 (tpm170) REVERT: B 59 THR cc_start: 0.2762 (t) cc_final: 0.2533 (t) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2258 time to fit residues: 10.7640 Evaluate side-chains 33 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** 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 = 0.5250 r_free = 0.5250 target = 0.299010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.298985 restraints weight = 8753.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.298985 restraints weight = 6309.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.298985 restraints weight = 6309.812| |-----------------------------------------------------------------------------| r_work (final): 0.5250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1594 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4398 Z= 0.202 Angle : 0.653 8.997 5990 Z= 0.347 Chirality : 0.047 0.218 666 Planarity : 0.006 0.052 772 Dihedral : 5.203 19.960 587 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.35), residues: 545 helix: -0.68 (0.85), residues: 41 sheet: -0.17 (0.38), residues: 192 loop : -1.39 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.002 PHE A 24 TYR 0.018 0.002 TYR A 103 ARG 0.008 0.001 ARG B 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1139.66 seconds wall clock time: 21 minutes 23.70 seconds (1283.70 seconds total)