Starting phenix.real_space_refine (version: dev) on Fri Feb 17 09:27:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/02_2023/5msh_3565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/02_2023/5msh_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_3565/02_2023/5msh_3565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/02_2023/5msh_3565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/02_2023/5msh_3565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5msh_3565/02_2023/5msh_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 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-4877/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: 2.73, per 1000 atoms: 0.64 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: 1.70 Conformation dependent library (CDL) restraints added in 583.0 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: 0.30 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: 1.17 Time building geometry restraints manager: 1.85 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.800 Check model and map are aligned: 0.060 Process input model: 15.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- 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 : 3.07 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 : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2334 time to fit residues: 18.2325 Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6458 ------------------------------------------------------------------------------- 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: 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: 4.5990 ------------------------------------------------------------------------------- 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: 0.0462 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4398 Z= 0.210 Angle : 0.698 8.917 5990 Z= 0.370 Chirality : 0.050 0.173 666 Planarity : 0.005 0.045 772 Dihedral : 5.403 28.292 587 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % 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: -0.44 (0.34), residues: 545 helix: -1.50 (0.68), residues: 51 sheet: 0.77 (0.39), residues: 176 loop : -0.69 (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 : 0.451 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1837 time to fit residues: 11.2360 Evaluate side-chains 30 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6849 ------------------------------------------------------------------------------- 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: 50.0000 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 50.0000 chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 50.0000 chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 39 optimal weight: 50.0000 overall best weight: 7.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0752 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 4398 Z= 0.262 Angle : 0.749 11.960 5990 Z= 0.398 Chirality : 0.053 0.553 666 Planarity : 0.006 0.059 772 Dihedral : 5.516 23.167 587 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.05 % Rotamer Outliers : 0.21 % 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: -0.40 (0.34), residues: 545 helix: -0.96 (0.78), residues: 46 sheet: 0.48 (0.38), residues: 181 loop : -0.57 (0.32), residues: 318 *********************** 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 45 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.475 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1617 time to fit residues: 9.7396 Evaluate side-chains 36 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0470 time to fit residues: 0.8411 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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: 0.0814 moved from start: 0.4954 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= 0.198 Angle : 0.630 9.011 5990 Z= 0.334 Chirality : 0.046 0.149 666 Planarity : 0.005 0.046 772 Dihedral : 5.265 23.704 587 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.78 % 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: -0.40 (0.34), residues: 545 helix: -0.85 (0.74), residues: 46 sheet: 0.37 (0.38), residues: 187 loop : -0.52 (0.33), 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 44 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1923 time to fit residues: 10.8616 Evaluate side-chains 34 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7095 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 overall best weight: 7.3588 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0953 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4398 Z= 0.233 Angle : 0.731 12.727 5990 Z= 0.382 Chirality : 0.050 0.206 666 Planarity : 0.005 0.045 772 Dihedral : 5.410 25.743 587 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % 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: -0.52 (0.35), residues: 545 helix: -0.82 (0.77), residues: 46 sheet: 0.56 (0.40), residues: 172 loop : -0.77 (0.32), residues: 327 *********************** 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 : 0.409 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1595 time to fit residues: 9.5046 Evaluate side-chains 38 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6776 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 0.0970 chunk 12 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 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: 0.0891 moved from start: 0.6107 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= 0.161 Angle : 0.590 9.155 5990 Z= 0.310 Chirality : 0.045 0.192 666 Planarity : 0.005 0.046 772 Dihedral : 4.962 19.829 587 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % 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: -0.52 (0.35), residues: 545 helix: -0.97 (0.70), residues: 53 sheet: 0.29 (0.38), residues: 189 loop : -0.59 (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 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1725 time to fit residues: 9.5306 Evaluate side-chains 36 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7144 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 20 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 33 optimal weight: 9.9990 overall best weight: 5.9666 ------------------------------------------------------------------------------- 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: 0.1005 moved from start: 0.6659 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= 0.195 Angle : 0.665 11.404 5990 Z= 0.345 Chirality : 0.048 0.206 666 Planarity : 0.005 0.049 772 Dihedral : 5.137 19.195 587 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.19 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: -0.75 (0.35), residues: 545 helix: -1.33 (0.74), residues: 47 sheet: 0.07 (0.39), residues: 193 loop : -0.67 (0.34), residues: 305 *********************** 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 44 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1734 time to fit residues: 9.8334 Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5961 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 50.0000 chunk 38 optimal weight: 0.4980 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0947 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4398 Z= 0.140 Angle : 0.569 8.301 5990 Z= 0.297 Chirality : 0.045 0.160 666 Planarity : 0.004 0.044 772 Dihedral : 4.665 18.593 587 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.18 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: -0.53 (0.36), residues: 545 helix: -1.22 (0.72), residues: 54 sheet: 0.30 (0.39), residues: 194 loop : -0.56 (0.35), residues: 297 *********************** 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 : 0.422 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1659 time to fit residues: 9.1495 Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6105 ------------------------------------------------------------------------------- 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: 50.0000 chunk 45 optimal weight: 40.0000 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 35 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** 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: 0.1191 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 4398 Z= 0.302 Angle : 0.822 16.788 5990 Z= 0.429 Chirality : 0.053 0.229 666 Planarity : 0.006 0.056 772 Dihedral : 5.783 27.998 587 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.97 % Favored : 92.84 % 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: -1.09 (0.35), residues: 545 helix: -1.41 (0.72), residues: 48 sheet: 0.19 (0.41), residues: 172 loop : -1.14 (0.33), residues: 325 *********************** 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 42 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.490 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1666 time to fit residues: 9.4625 Evaluate side-chains 39 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7303 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 13 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 0.0020 chunk 42 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 overall best weight: 2.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN ** 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: 0.1061 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 4398 Z= 0.155 Angle : 0.601 10.166 5990 Z= 0.312 Chirality : 0.046 0.169 666 Planarity : 0.005 0.044 772 Dihedral : 4.913 24.030 587 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer Outliers : 0.21 % 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: -0.82 (0.36), residues: 545 helix: -0.89 (0.76), residues: 48 sheet: 0.01 (0.40), residues: 185 loop : -0.79 (0.34), residues: 312 ********************** 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 41 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.516 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1971 time to fit residues: 10.5446 Evaluate side-chains 35 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7175 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 50.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5270 r_free = 0.5270 target = 0.300221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.299129 restraints weight = 8638.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.298538 restraints weight = 7825.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5252 r_free = 0.5252 target = 0.298771 restraints weight = 5848.342| |-----------------------------------------------------------------------------| r_work (final): 0.5254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1555 moved from start: 0.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 4398 Z= 0.266 Angle : 0.767 15.861 5990 Z= 0.403 Chirality : 0.051 0.211 666 Planarity : 0.006 0.059 772 Dihedral : 5.501 29.017 587 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.79 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: -1.06 (0.35), residues: 545 helix: -0.54 (0.91), residues: 36 sheet: 0.04 (0.40), residues: 176 loop : -1.17 (0.32), residues: 333 =============================================================================== Job complete usr+sys time: 1103.30 seconds wall clock time: 20 minutes 49.05 seconds (1249.05 seconds total)