Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:28:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/11_2022/5msh_3565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/11_2022/5msh_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_3565/11_2022/5msh_3565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/11_2022/5msh_3565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/11_2022/5msh_3565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/11_2022/5msh_3565.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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: 2.95, per 1000 atoms: 0.69 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: 1.78 Conformation dependent library (CDL) restraints added in 658.6 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: 0.32 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: 1.18 Time building geometry restraints manager: 1.92 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 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. 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: 2.030 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: 11.550 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 17.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0184 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= 1.031 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 : 3.19 Ramachandran Plot: Outliers : 1.47 % Allowed : 6.06 % Favored : 92.48 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2328 time to fit residues: 18.2698 Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7397 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 10.0000 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: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0473 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4398 Z= 0.215 Angle : 0.690 8.637 5990 Z= 0.369 Chirality : 0.049 0.159 666 Planarity : 0.005 0.046 772 Dihedral : 5.356 27.900 587 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.41 % Rotamer Outliers : 0.00 % 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: -0.42 (0.34), residues: 545 helix: -1.43 (0.69), residues: 51 sheet: 0.81 (0.39), residues: 176 loop : -0.71 (0.32), residues: 318 *********************** 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 47 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1729 time to fit residues: 10.6398 Evaluate side-chains 32 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7193 ------------------------------------------------------------------------------- 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: 40.0000 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 50.0000 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 16 optimal weight: 0.1980 chunk 39 optimal weight: 40.0000 overall best weight: 7.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0768 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 4398 Z= 0.267 Angle : 0.757 13.093 5990 Z= 0.401 Chirality : 0.051 0.316 666 Planarity : 0.006 0.056 772 Dihedral : 5.683 23.341 587 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.22 % Favored : 95.60 % Rotamer Outliers : 0.63 % 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: -0.56 (0.34), residues: 545 helix: -1.25 (0.78), residues: 46 sheet: 0.39 (0.39), residues: 184 loop : -0.67 (0.32), residues: 315 *********************** 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 46 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1795 time to fit residues: 10.6205 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0580 time to fit residues: 0.9982 ------------------------------------------------------------------------------- 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: 50.0000 chunk 36 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** 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: 0.0937 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 4398 Z= 0.254 Angle : 0.732 13.046 5990 Z= 0.386 Chirality : 0.050 0.295 666 Planarity : 0.006 0.054 772 Dihedral : 5.752 25.534 587 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Rotamer Outliers : 1.05 % 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: -0.81 (0.34), residues: 545 helix: -0.92 (0.78), residues: 46 sheet: 0.16 (0.38), residues: 187 loop : -0.89 (0.32), residues: 312 *********************** 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 53 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1912 time to fit residues: 12.9225 Evaluate side-chains 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0525 time to fit residues: 1.0788 ------------------------------------------------------------------------------- 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: 40.0000 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 40.0000 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 157 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0991 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4398 Z= 0.210 Angle : 0.673 11.727 5990 Z= 0.354 Chirality : 0.047 0.221 666 Planarity : 0.005 0.053 772 Dihedral : 5.361 24.015 587 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Rotamer Outliers : 0.00 % 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: -0.68 (0.35), residues: 545 helix: -0.91 (0.76), residues: 46 sheet: 0.16 (0.39), residues: 192 loop : -0.73 (0.33), residues: 307 *********************** 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 45 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1572 time to fit residues: 9.5450 Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7208 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0939 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 4398 Z= 0.154 Angle : 0.585 8.800 5990 Z= 0.305 Chirality : 0.046 0.181 666 Planarity : 0.005 0.053 772 Dihedral : 4.852 21.529 587 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.94 % Rotamer Outliers : 0.00 % 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: -0.63 (0.35), residues: 545 helix: -1.07 (0.70), residues: 53 sheet: 0.27 (0.39), residues: 189 loop : -0.70 (0.34), residues: 303 *********************** 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 : 0.525 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1665 time to fit residues: 10.2038 Evaluate side-chains 36 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6815 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 50.0000 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 50.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1021 moved from start: 0.6971 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= 0.194 Angle : 0.646 11.804 5990 Z= 0.335 Chirality : 0.048 0.196 666 Planarity : 0.005 0.049 772 Dihedral : 5.020 19.687 587 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.16 % Favored : 92.66 % Rotamer Outliers : 0.00 % 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: -0.72 (0.35), residues: 545 helix: -0.89 (0.82), residues: 41 sheet: -0.00 (0.39), residues: 193 loop : -0.68 (0.34), residues: 311 *********************** 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 : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1830 time to fit residues: 10.0251 Evaluate side-chains 39 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7362 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 0.0770 chunk 40 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 49 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 40.0000 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 overall best weight: 5.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1068 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4398 Z= 0.197 Angle : 0.628 10.673 5990 Z= 0.326 Chirality : 0.046 0.182 666 Planarity : 0.005 0.049 772 Dihedral : 4.933 21.286 587 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.79 % Favored : 93.03 % Rotamer Outliers : 0.00 % 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: -0.86 (0.35), residues: 545 helix: -0.81 (0.77), residues: 47 sheet: -0.14 (0.38), residues: 193 loop : -0.77 (0.34), residues: 305 *********************** 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 : 0.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1895 time to fit residues: 10.3123 Evaluate side-chains 37 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5424 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 40.0000 chunk 31 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 50.0000 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 overall best weight: 7.3188 ------------------------------------------------------------------------------- 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: 0.1141 moved from start: 0.7900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4398 Z= 0.233 Angle : 0.717 14.202 5990 Z= 0.367 Chirality : 0.048 0.185 666 Planarity : 0.006 0.053 772 Dihedral : 5.174 23.655 587 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.71 % Favored : 92.11 % Rotamer Outliers : 0.00 % 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: -1.08 (0.35), residues: 545 helix: -1.11 (0.75), residues: 47 sheet: -0.20 (0.39), residues: 193 loop : -0.96 (0.34), residues: 305 *********************** 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 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1745 time to fit residues: 9.2832 Evaluate side-chains 36 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7360 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1123 moved from start: 0.8103 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= 0.190 Angle : 0.655 11.056 5990 Z= 0.336 Chirality : 0.046 0.164 666 Planarity : 0.005 0.053 772 Dihedral : 4.973 23.202 587 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.39 % Rotamer Outliers : 0.00 % 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: -0.95 (0.36), residues: 545 helix: -0.41 (0.87), residues: 40 sheet: -0.17 (0.38), residues: 195 loop : -0.94 (0.34), residues: 310 ********************** 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 : 0.515 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1640 time to fit residues: 8.5025 Evaluate side-chains 34 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7251 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.301097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.296998 restraints weight = 8600.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.297774 restraints weight = 6566.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.298294 restraints weight = 4965.493| |-----------------------------------------------------------------------------| r_work (final): 0.5239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1477 moved from start: 0.8267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4398 Z= 0.172 Angle : 0.632 10.673 5990 Z= 0.325 Chirality : 0.046 0.222 666 Planarity : 0.005 0.050 772 Dihedral : 4.777 22.324 587 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer Outliers : 0.00 % 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: -0.94 (0.36), residues: 545 helix: -0.17 (0.96), residues: 35 sheet: -0.09 (0.39), residues: 192 loop : -1.01 (0.33), residues: 318 =============================================================================== Job complete usr+sys time: 1073.59 seconds wall clock time: 20 minutes 59.24 seconds (1259.24 seconds total)