Starting phenix.real_space_refine on Mon Sep 23 21:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsi_32759/09_2024/7wsi_32759.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3678 2.51 5 N 913 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5701 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2348 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.69, per 1000 atoms: 0.65 Number of scatterers: 5701 At special positions: 0 Unit cell: (87.15, 72.21, 141.93, 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 43 16.00 O 1067 8.00 N 913 7.00 C 3678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.61 Conformation dependent library (CDL) restraints added in 627.8 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 38.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.758A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.565A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.888A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.568A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.587A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.675A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.520A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.104A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 4.367A pdb=" N SER H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.547A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.610A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.324A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.868A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.009A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 4.016A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 removed outlier: 6.077A pdb=" N HIS L 203 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER L 208 " --> pdb=" O HIS L 203 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 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: 1.23 - 1.35: 1736 1.35 - 1.46: 1445 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5839 Sorted by residual: bond pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 1.520 1.513 0.008 7.30e-03 1.88e+04 1.06e+00 bond pdb=" N SER L 25 " pdb=" CA SER L 25 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.89e-01 bond pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" SD MET A 122 " pdb=" CE MET A 122 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.33e-01 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7474 1.21 - 2.43: 343 2.43 - 3.64: 78 3.64 - 4.85: 26 4.85 - 6.07: 13 Bond angle restraints: 7934 Sorted by residual: angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 111.77 108.04 3.73 1.04e+00 9.25e-01 1.29e+01 angle pdb=" C PRO L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.98e+00 angle pdb=" CA CYS L 94 " pdb=" CB CYS L 94 " pdb=" SG CYS L 94 " ideal model delta sigma weight residual 114.40 120.23 -5.83 2.30e+00 1.89e-01 6.43e+00 angle pdb=" C ASP A 149 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.82e+00 angle pdb=" N THR L 169 " pdb=" CA THR L 169 " pdb=" C THR L 169 " ideal model delta sigma weight residual 110.53 107.76 2.77 1.29e+00 6.01e-01 4.61e+00 ... (remaining 7929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 3061 13.97 - 27.94: 325 27.94 - 41.91: 84 41.91 - 55.87: 12 55.87 - 69.84: 2 Dihedral angle restraints: 3484 sinusoidal: 1332 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 158.44 -65.44 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual -86.00 -118.30 32.30 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA TYR L 92 " pdb=" C TYR L 92 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 559 0.032 - 0.064: 241 0.064 - 0.096: 77 0.096 - 0.127: 37 0.127 - 0.159: 4 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 915 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " 0.041 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO L 65 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 181 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO L 50 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.020 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 5605 3.23 - 3.79: 8449 3.79 - 4.34: 11132 4.34 - 4.90: 18947 Nonbonded interactions: 44215 Sorted by model distance: nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.122 3.120 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.229 3.040 nonbonded pdb=" NE2 GLN L 96 " pdb=" OG1 THR L 102 " model vdw 2.328 3.120 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.340 3.120 nonbonded pdb=" O TYR L 55 " pdb=" OG1 THR L 59 " model vdw 2.354 3.040 ... (remaining 44210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.003 0.027 5839 Z= 0.199 Angle : 0.668 6.068 7934 Z= 0.349 Chirality : 0.043 0.159 918 Planarity : 0.005 0.063 981 Dihedral : 12.247 69.843 2099 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.32), residues: 737 helix: 0.97 (0.34), residues: 241 sheet: 0.43 (0.39), residues: 195 loop : -1.50 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 41 HIS 0.002 0.001 HIS H 106 PHE 0.018 0.001 PHE A 292 TYR 0.017 0.002 TYR A 69 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TRP cc_start: 0.5403 (m-10) cc_final: 0.5077 (m-10) REVERT: H 3 GLN cc_start: 0.7813 (pp30) cc_final: 0.7395 (pp30) REVERT: H 117 LEU cc_start: 0.8462 (tt) cc_final: 0.8099 (tp) REVERT: L 42 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80) REVERT: L 44 GLN cc_start: 0.8043 (tt0) cc_final: 0.7616 (tt0) REVERT: L 128 GLU cc_start: 0.7847 (pm20) cc_final: 0.7550 (pm20) REVERT: L 143 ASN cc_start: 0.8175 (m-40) cc_final: 0.7957 (m-40) REVERT: L 160 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7635 (ptp90) REVERT: L 168 TRP cc_start: 0.8956 (m-90) cc_final: 0.8650 (m-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1618 time to fit residues: 62.0232 Evaluate side-chains 234 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 39 GLN L 6 GLN L 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5839 Z= 0.238 Angle : 0.733 7.630 7934 Z= 0.367 Chirality : 0.045 0.155 918 Planarity : 0.005 0.077 981 Dihedral : 4.642 16.416 794 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.19 % Favored : 92.67 % Rotamer: Outliers : 4.64 % Allowed : 16.38 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.31), residues: 737 helix: 0.87 (0.34), residues: 252 sheet: 0.44 (0.40), residues: 182 loop : -1.75 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.002 0.001 HIS L 203 PHE 0.015 0.001 PHE A 292 TYR 0.021 0.002 TYR L 98 ARG 0.006 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 226 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7543 (tt) cc_final: 0.6764 (tt) REVERT: A 223 ILE cc_start: 0.8574 (mp) cc_final: 0.8232 (mt) REVERT: A 246 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8076 (mm) REVERT: H 3 GLN cc_start: 0.7851 (pp30) cc_final: 0.7522 (pp30) REVERT: H 55 ASN cc_start: 0.8198 (p0) cc_final: 0.7993 (p0) REVERT: H 117 LEU cc_start: 0.8357 (tt) cc_final: 0.8063 (tp) REVERT: H 130 TYR cc_start: 0.8418 (m-10) cc_final: 0.8208 (m-80) REVERT: L 198 THR cc_start: 0.8032 (m) cc_final: 0.7708 (p) outliers start: 30 outliers final: 19 residues processed: 236 average time/residue: 0.1432 time to fit residues: 45.4520 Evaluate side-chains 233 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 53 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 247 ASN L 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5839 Z= 0.366 Angle : 0.752 8.388 7934 Z= 0.377 Chirality : 0.047 0.149 918 Planarity : 0.005 0.051 981 Dihedral : 4.903 18.547 794 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.65 % Allowed : 20.87 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.31), residues: 737 helix: 0.74 (0.33), residues: 255 sheet: 0.44 (0.41), residues: 166 loop : -1.78 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 305 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.002 PHE H 154 TYR 0.027 0.002 TYR H 183 ARG 0.004 0.001 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 246 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7969 (mt) REVERT: H 3 GLN cc_start: 0.8002 (pp30) cc_final: 0.7643 (pp30) REVERT: H 130 TYR cc_start: 0.8599 (m-10) cc_final: 0.8238 (m-80) REVERT: L 123 PHE cc_start: 0.8977 (m-80) cc_final: 0.8763 (m-80) REVERT: L 161 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7940 (tm-30) REVERT: L 180 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7601 (tpt) outliers start: 43 outliers final: 32 residues processed: 234 average time/residue: 0.1394 time to fit residues: 43.5051 Evaluate side-chains 243 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain L residue 212 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5839 Z= 0.194 Angle : 0.701 8.698 7934 Z= 0.342 Chirality : 0.045 0.156 918 Planarity : 0.004 0.043 981 Dihedral : 4.584 17.333 794 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.79 % Allowed : 24.73 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.31), residues: 737 helix: 0.92 (0.34), residues: 254 sheet: 0.63 (0.42), residues: 166 loop : -1.70 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.001 PHE A 292 TYR 0.021 0.002 TYR H 183 ARG 0.005 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7784 (tt) cc_final: 0.7143 (tt) REVERT: A 223 ILE cc_start: 0.8521 (mp) cc_final: 0.8284 (mt) REVERT: A 246 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7937 (mm) REVERT: H 3 GLN cc_start: 0.7909 (pp30) cc_final: 0.7595 (pp30) REVERT: H 130 TYR cc_start: 0.8348 (m-80) cc_final: 0.7984 (m-80) REVERT: L 161 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7597 (tm-30) REVERT: L 168 TRP cc_start: 0.8980 (m-90) cc_final: 0.8770 (m-90) REVERT: L 180 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7811 (tpt) outliers start: 31 outliers final: 21 residues processed: 239 average time/residue: 0.1424 time to fit residues: 45.9570 Evaluate side-chains 238 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 52 optimal weight: 0.0050 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5839 Z= 0.202 Angle : 0.701 12.059 7934 Z= 0.339 Chirality : 0.044 0.167 918 Planarity : 0.004 0.036 981 Dihedral : 4.477 16.628 794 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.41 % Allowed : 25.50 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 737 helix: 0.97 (0.34), residues: 255 sheet: 0.71 (0.42), residues: 166 loop : -1.69 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.022 0.002 TYR H 183 ARG 0.003 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6705 (mtp) cc_final: 0.6464 (mtp) REVERT: A 141 TYR cc_start: 0.7923 (m-80) cc_final: 0.7712 (m-80) REVERT: A 197 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (tp) REVERT: A 223 ILE cc_start: 0.8451 (mp) cc_final: 0.8233 (mt) REVERT: A 246 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7221 (mp) REVERT: H 3 GLN cc_start: 0.7928 (pp30) cc_final: 0.7679 (pp30) REVERT: H 130 TYR cc_start: 0.8310 (m-80) cc_final: 0.8066 (m-80) REVERT: L 161 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7625 (tm-30) REVERT: L 168 TRP cc_start: 0.8964 (m-90) cc_final: 0.8733 (m-90) REVERT: L 180 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7752 (tpt) outliers start: 35 outliers final: 20 residues processed: 221 average time/residue: 0.1378 time to fit residues: 41.2617 Evaluate side-chains 227 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5839 Z= 0.196 Angle : 0.674 8.067 7934 Z= 0.331 Chirality : 0.044 0.171 918 Planarity : 0.004 0.037 981 Dihedral : 4.438 19.273 794 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.17 % Allowed : 28.28 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.32), residues: 737 helix: 1.12 (0.34), residues: 254 sheet: 0.72 (0.43), residues: 166 loop : -1.71 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.023 0.002 TYR H 183 ARG 0.004 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8885 (tp) cc_final: 0.8658 (tp) REVERT: A 141 TYR cc_start: 0.7928 (m-80) cc_final: 0.7687 (m-80) REVERT: A 223 ILE cc_start: 0.8430 (mp) cc_final: 0.8210 (mt) REVERT: A 246 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.6944 (tp) REVERT: H 3 GLN cc_start: 0.7929 (pp30) cc_final: 0.7687 (pp30) REVERT: H 130 TYR cc_start: 0.8058 (m-80) cc_final: 0.7613 (m-10) REVERT: H 215 ASP cc_start: 0.7614 (t0) cc_final: 0.6918 (p0) REVERT: L 129 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7574 (tm-30) REVERT: L 161 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7717 (tm-30) REVERT: L 168 TRP cc_start: 0.8936 (m-90) cc_final: 0.8711 (m-90) REVERT: L 180 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7843 (tpt) outliers start: 27 outliers final: 18 residues processed: 223 average time/residue: 0.1342 time to fit residues: 40.7967 Evaluate side-chains 228 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 70 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 28 optimal weight: 0.5980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5839 Z= 0.189 Angle : 0.696 10.763 7934 Z= 0.336 Chirality : 0.044 0.183 918 Planarity : 0.004 0.035 981 Dihedral : 4.367 16.564 794 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.17 % Allowed : 28.28 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.32), residues: 737 helix: 1.11 (0.34), residues: 254 sheet: 0.63 (0.42), residues: 175 loop : -1.68 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.021 0.001 PHE A 292 TYR 0.021 0.001 TYR L 98 ARG 0.003 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7633 (tt) cc_final: 0.6978 (tt) REVERT: H 3 GLN cc_start: 0.7908 (pp30) cc_final: 0.7668 (pp30) REVERT: H 130 TYR cc_start: 0.7987 (m-80) cc_final: 0.7657 (m-10) REVERT: H 215 ASP cc_start: 0.7544 (t70) cc_final: 0.6845 (p0) REVERT: L 87 GLU cc_start: 0.7848 (pp20) cc_final: 0.7279 (pp20) REVERT: L 129 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7463 (tm-30) REVERT: L 161 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7537 (tm-30) REVERT: L 180 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7881 (tpt) outliers start: 27 outliers final: 15 residues processed: 235 average time/residue: 0.1279 time to fit residues: 41.2576 Evaluate side-chains 221 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN L 6 GLN L 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5839 Z= 0.212 Angle : 0.730 10.059 7934 Z= 0.350 Chirality : 0.045 0.182 918 Planarity : 0.004 0.036 981 Dihedral : 4.383 16.829 794 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.55 % Allowed : 29.68 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.32), residues: 737 helix: 1.09 (0.34), residues: 254 sheet: 0.61 (0.42), residues: 175 loop : -1.68 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.001 PHE A 18 TYR 0.022 0.002 TYR H 183 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: H 130 TYR cc_start: 0.8011 (m-80) cc_final: 0.7679 (m-10) REVERT: H 215 ASP cc_start: 0.7578 (t70) cc_final: 0.6854 (p0) REVERT: L 87 GLU cc_start: 0.7882 (pp20) cc_final: 0.7239 (pp20) REVERT: L 129 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7386 (tm-30) REVERT: L 161 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7466 (tm-30) REVERT: L 180 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8031 (tpt) outliers start: 23 outliers final: 18 residues processed: 216 average time/residue: 0.1286 time to fit residues: 38.3678 Evaluate side-chains 220 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 117 ASN A 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5839 Z= 0.291 Angle : 0.753 9.749 7934 Z= 0.371 Chirality : 0.046 0.187 918 Planarity : 0.004 0.036 981 Dihedral : 4.642 17.539 794 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.55 % Allowed : 29.52 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.32), residues: 737 helix: 1.03 (0.34), residues: 254 sheet: 0.51 (0.41), residues: 184 loop : -1.69 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 168 HIS 0.002 0.001 HIS H 35 PHE 0.025 0.002 PHE A 292 TYR 0.022 0.002 TYR L 98 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6203 (mtp) cc_final: 0.5789 (mtp) REVERT: A 91 LEU cc_start: 0.8890 (tp) cc_final: 0.8625 (tp) REVERT: A 246 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7399 (mt) REVERT: H 130 TYR cc_start: 0.8012 (m-80) cc_final: 0.7665 (m-10) REVERT: L 129 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7486 (tm-30) REVERT: L 159 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8163 (mm-30) REVERT: L 161 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7539 (tm-30) REVERT: L 180 MET cc_start: 0.8513 (tpt) cc_final: 0.7979 (tpt) outliers start: 23 outliers final: 17 residues processed: 212 average time/residue: 0.1561 time to fit residues: 45.3078 Evaluate side-chains 220 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5839 Z= 0.222 Angle : 0.755 10.003 7934 Z= 0.368 Chirality : 0.046 0.203 918 Planarity : 0.004 0.037 981 Dihedral : 4.597 18.966 794 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.47 % Allowed : 30.45 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 737 helix: 1.04 (0.34), residues: 252 sheet: 0.57 (0.42), residues: 176 loop : -1.61 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.037 0.001 PHE A 274 TYR 0.022 0.002 TYR L 98 ARG 0.007 0.001 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 130 TYR cc_start: 0.8004 (m-80) cc_final: 0.7693 (m-10) REVERT: L 129 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7425 (tm-30) REVERT: L 161 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7462 (tm-30) REVERT: L 180 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8043 (tpt) outliers start: 16 outliers final: 14 residues processed: 212 average time/residue: 0.1352 time to fit residues: 39.1647 Evaluate side-chains 219 residues out of total 647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110797 restraints weight = 10836.672| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.49 r_work: 0.3244 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5839 Z= 0.216 Angle : 0.750 9.809 7934 Z= 0.363 Chirality : 0.046 0.204 918 Planarity : 0.004 0.034 981 Dihedral : 4.557 18.175 794 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.94 % Allowed : 30.45 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.32), residues: 737 helix: 1.04 (0.34), residues: 253 sheet: 0.61 (0.42), residues: 176 loop : -1.61 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.036 0.002 PHE A 274 TYR 0.022 0.002 TYR L 98 ARG 0.002 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.97 seconds wall clock time: 31 minutes 6.53 seconds (1866.53 seconds total)