Starting phenix.real_space_refine on Tue Nov 14 17:18:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk6_25174/11_2023/7sk6_25174_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 3052 2.51 5 N 766 2.21 5 O 833 1.98 5 H 4462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4799 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 987 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1507 Classifications: {'peptide': 101} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "F" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1851 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 4.56, per 1000 atoms: 0.50 Number of scatterers: 9144 At special positions: 0 Unit cell: (61.56, 66.96, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 833 8.00 N 766 7.00 C 3052 6.00 H 4462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.02 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1118 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 46.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 39 through 76 removed outlier: 3.837A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.748A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 4.041A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 4.074A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.519A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.184A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.963A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.719A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix removed outlier: 3.748A pdb=" N TYR A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'B' and resid 2 through 7 removed outlier: 4.035A pdb=" N TYR B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'F' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.510A pdb=" N VAL B 49 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.537A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.734A pdb=" N TYR A 195 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.754A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.608A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 5.985A pdb=" N GLY F 13 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4452 1.04 - 1.24: 594 1.24 - 1.43: 1575 1.43 - 1.63: 2607 1.63 - 1.83: 42 Bond restraints: 9270 Sorted by residual: bond pdb=" ND1 HIS A 248 " pdb=" CE1 HIS A 248 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" ND1 HIS A 107 " pdb=" CE1 HIS A 107 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.29e+01 bond pdb=" ND1 HIS A 269 " pdb=" CE1 HIS A 269 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" ND1 HIS A 203 " pdb=" CE1 HIS A 203 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" ND1 HIS A 291 " pdb=" CE1 HIS A 291 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 ... (remaining 9265 not shown) Histogram of bond angle deviations from ideal: 91.98 - 100.35: 15 100.35 - 108.73: 3558 108.73 - 117.10: 8220 117.10 - 125.48: 4651 125.48 - 133.85: 172 Bond angle restraints: 16616 Sorted by residual: angle pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N PRO A 98 " ideal model delta sigma weight residual 120.83 125.23 -4.40 6.10e-01 2.69e+00 5.20e+01 angle pdb=" N LYS F 79 " pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 108.90 98.42 10.48 1.63e+00 3.76e-01 4.13e+01 angle pdb=" N VAL B 39 " pdb=" CA VAL B 39 " pdb=" C VAL B 39 " ideal model delta sigma weight residual 108.81 98.54 10.27 1.62e+00 3.81e-01 4.02e+01 angle pdb=" C ILE A 210 " pdb=" N GLY A 211 " pdb=" CA GLY A 211 " ideal model delta sigma weight residual 119.99 126.87 -6.88 1.13e+00 7.83e-01 3.70e+01 angle pdb=" C ILE A 205 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " ideal model delta sigma weight residual 120.79 129.21 -8.42 1.39e+00 5.18e-01 3.67e+01 ... (remaining 16611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3685 17.49 - 34.97: 111 34.97 - 52.46: 21 52.46 - 69.95: 26 69.95 - 87.43: 4 Dihedral angle restraints: 3847 sinusoidal: 1691 harmonic: 2156 Sorted by residual: dihedral pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CA HIS A 281 " pdb=" CB HIS A 281 " ideal model delta harmonic sigma weight residual 122.80 133.20 -10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA THR A 147 " pdb=" C THR A 147 " pdb=" N TYR A 148 " pdb=" CA TYR A 148 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C ILE A 146 " pdb=" N ILE A 146 " pdb=" CA ILE A 146 " pdb=" CB ILE A 146 " ideal model delta harmonic sigma weight residual -122.00 -131.85 9.85 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 480 0.093 - 0.186: 203 0.186 - 0.279: 51 0.279 - 0.373: 10 0.373 - 0.466: 3 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA HIS A 281 " pdb=" N HIS A 281 " pdb=" C HIS A 281 " pdb=" CB HIS A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA THR A 300 " pdb=" N THR A 300 " pdb=" C THR A 300 " pdb=" CB THR A 300 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN A 127 " pdb=" N ASN A 127 " pdb=" C ASN A 127 " pdb=" CB ASN A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 744 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 109 " -0.146 2.00e-02 2.50e+03 5.67e-02 1.29e+02 pdb=" CG TRP F 109 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 109 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP F 109 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP F 109 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP F 109 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 109 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 109 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 109 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 TRP F 109 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP F 109 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP F 109 " 0.008 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 109 " -0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 109 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP F 109 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 83 " 0.094 2.00e-02 2.50e+03 4.09e-02 5.01e+01 pdb=" CG TYR F 83 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR F 83 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR F 83 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR F 83 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 83 " 0.077 2.00e-02 2.50e+03 pdb=" HD1 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR F 83 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR F 83 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR F 83 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 322 " -0.093 2.00e-02 2.50e+03 3.92e-02 4.62e+01 pdb=" CG TYR A 322 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 322 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 322 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 322 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 322 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 322 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 322 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 322 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 322 " 0.001 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 584 2.25 - 2.83: 19486 2.83 - 3.42: 24520 3.42 - 4.01: 32883 4.01 - 4.60: 49936 Nonbonded interactions: 127409 Sorted by model distance: nonbonded pdb=" H THR A 150 " pdb=" H ASN A 151 " model vdw 1.658 2.100 nonbonded pdb=" H ASN B 45 " pdb=" H ASN B 46 " model vdw 1.661 2.100 nonbonded pdb=" H ALA E 52 " pdb=" H SER E 53 " model vdw 1.689 2.100 nonbonded pdb=" H SER E 53 " pdb=" H SER E 54 " model vdw 1.705 2.100 nonbonded pdb=" H LYS B 54 " pdb=" H LEU B 55 " model vdw 1.727 2.100 ... (remaining 127404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.130 Extract box with map and model: 7.470 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 : 0.018 0.045 4808 Z= 1.167 Angle : 1.923 10.476 6545 Z= 1.309 Chirality : 0.111 0.466 747 Planarity : 0.014 0.089 796 Dihedral : 13.164 87.433 1684 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 1.75 % Allowed : 4.20 % Favored : 94.05 % Rotamer: Outliers : 0.76 % Allowed : 1.71 % Favored : 97.53 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.36), residues: 571 helix: 2.83 (0.32), residues: 245 sheet: -1.42 (0.46), residues: 117 loop : -2.05 (0.36), residues: 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.4512 time to fit residues: 61.2001 Evaluate side-chains 79 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3552 time to fit residues: 1.8294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 245 GLN F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.197 Angle : 0.608 5.021 6545 Z= 0.339 Chirality : 0.043 0.170 747 Planarity : 0.005 0.042 796 Dihedral : 5.290 25.206 638 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.97 % Rotamer: Outliers : 1.33 % Allowed : 7.60 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.35), residues: 571 helix: 2.73 (0.31), residues: 245 sheet: -1.21 (0.48), residues: 113 loop : -1.58 (0.37), residues: 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.3469 time to fit residues: 37.1695 Evaluate side-chains 75 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.732 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1238 time to fit residues: 2.1928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 7 GLN F 16 GLN F 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4808 Z= 0.185 Angle : 0.554 5.075 6545 Z= 0.302 Chirality : 0.041 0.162 747 Planarity : 0.004 0.032 796 Dihedral : 4.933 24.283 638 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 8.37 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.35), residues: 571 helix: 2.75 (0.31), residues: 245 sheet: -1.14 (0.50), residues: 111 loop : -1.41 (0.38), residues: 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.3170 time to fit residues: 31.9797 Evaluate side-chains 75 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.806 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1304 time to fit residues: 2.2528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4808 Z= 0.294 Angle : 0.582 4.340 6545 Z= 0.327 Chirality : 0.041 0.158 747 Planarity : 0.004 0.035 796 Dihedral : 5.074 25.333 638 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.57 % Allowed : 9.51 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.35), residues: 571 helix: 2.34 (0.31), residues: 246 sheet: -1.50 (0.49), residues: 111 loop : -1.50 (0.38), residues: 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.2968 time to fit residues: 27.8426 Evaluate side-chains 68 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.812 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1384 time to fit residues: 1.6425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4808 Z= 0.248 Angle : 0.556 5.147 6545 Z= 0.308 Chirality : 0.041 0.155 747 Planarity : 0.004 0.040 796 Dihedral : 4.949 24.636 638 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 10.08 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.35), residues: 571 helix: 2.42 (0.31), residues: 245 sheet: -1.63 (0.50), residues: 111 loop : -1.50 (0.39), residues: 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.2925 time to fit residues: 26.2639 Evaluate side-chains 65 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.847 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1437 time to fit residues: 1.9009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4808 Z= 0.373 Angle : 0.645 4.958 6545 Z= 0.365 Chirality : 0.042 0.149 747 Planarity : 0.005 0.041 796 Dihedral : 5.378 27.325 638 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.52 % Allowed : 9.70 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.34), residues: 571 helix: 1.70 (0.31), residues: 244 sheet: -2.01 (0.49), residues: 111 loop : -2.04 (0.38), residues: 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.2848 time to fit residues: 23.9064 Evaluate side-chains 61 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.801 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1298 time to fit residues: 2.2364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4808 Z= 0.175 Angle : 0.528 4.390 6545 Z= 0.291 Chirality : 0.041 0.164 747 Planarity : 0.004 0.040 796 Dihedral : 4.881 19.124 638 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.38 % Allowed : 10.65 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.36), residues: 571 helix: 2.42 (0.31), residues: 245 sheet: -1.92 (0.50), residues: 113 loop : -1.60 (0.41), residues: 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.2801 time to fit residues: 24.0945 Evaluate side-chains 58 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.817 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1933 time to fit residues: 1.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.169 Angle : 0.505 4.066 6545 Z= 0.278 Chirality : 0.040 0.157 747 Planarity : 0.004 0.039 796 Dihedral : 4.697 19.389 638 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 11.03 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.37), residues: 571 helix: 2.58 (0.31), residues: 245 sheet: -1.66 (0.52), residues: 111 loop : -1.43 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.2839 time to fit residues: 24.1513 Evaluate side-chains 61 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.791 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1496 time to fit residues: 1.6584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4808 Z= 0.160 Angle : 0.493 4.165 6545 Z= 0.270 Chirality : 0.040 0.157 747 Planarity : 0.004 0.038 796 Dihedral : 4.554 18.405 638 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.38 % Allowed : 11.03 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 571 helix: 2.62 (0.32), residues: 245 sheet: -1.63 (0.52), residues: 113 loop : -1.29 (0.42), residues: 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.2822 time to fit residues: 23.6210 Evaluate side-chains 59 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.784 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1900 time to fit residues: 1.2142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.171 Angle : 0.491 4.021 6545 Z= 0.270 Chirality : 0.040 0.156 747 Planarity : 0.004 0.037 796 Dihedral : 4.507 18.262 638 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.38 % Allowed : 11.60 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.37), residues: 571 helix: 2.63 (0.32), residues: 245 sheet: -1.62 (0.52), residues: 113 loop : -1.28 (0.42), residues: 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue ILE 88 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 132 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue ILE 205 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 227 is missing expected H atoms. Skipping. Residue ILE 228 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 283 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 38 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 58 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue ILE 22 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue ILE 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.2957 time to fit residues: 24.6163 Evaluate side-chains 60 residues out of total 526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.858 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1762 time to fit residues: 1.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.066994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.061524 restraints weight = 90739.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.063186 restraints weight = 46411.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064280 restraints weight = 27727.367| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4808 Z= 0.172 Angle : 0.490 4.082 6545 Z= 0.270 Chirality : 0.040 0.156 747 Planarity : 0.004 0.037 796 Dihedral : 4.471 17.973 638 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.19 % Allowed : 11.98 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.37), residues: 571 helix: 2.64 (0.32), residues: 245 sheet: -1.60 (0.52), residues: 113 loop : -1.27 (0.42), residues: 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.05 seconds wall clock time: 50 minutes 19.75 seconds (3019.75 seconds total)