Starting phenix.real_space_refine on Wed Mar 5 23:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk8_32562/03_2025/7wk8_32562.cif" } resolution = 3.61 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= 0.011 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 16 5.16 5 C 2512 2.51 5 N 671 2.21 5 O 783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3982 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 150 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Time building chain proxies: 4.10, per 1000 atoms: 1.03 Number of scatterers: 3982 At special positions: 0 Unit cell: (96.184, 95.091, 61.208, 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 16 16.00 O 783 8.00 N 671 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 505.7 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 3.3% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 127 through 132 removed outlier: 4.250A pdb=" N SER D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 132' Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.977A pdb=" N ARG D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.571A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.570A pdb=" N VAL C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 92 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET C 34 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N MET C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.570A pdb=" N VAL C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 92 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG C 98 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.775A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 182 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.584A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 21 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS D 23 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 76 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.580A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 51 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.580A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS D 94 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA D 101 " --> pdb=" O HIS D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.741A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER D 180 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 166 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.897A pdb=" N TYR D 196 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 213 " --> pdb=" O TYR D 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.538A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 315 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: 1.14 Time building geometry restraints manager: 1.16 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: 1262 1.35 - 1.46: 998 1.46 - 1.58: 1799 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4081 Sorted by residual: bond pdb=" N LEU C 184 " pdb=" CA LEU C 184 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.18e+00 bond pdb=" N THR C 183 " pdb=" CA THR C 183 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.26e-02 6.30e+03 7.73e+00 bond pdb=" C GLU D 109 " pdb=" N ILE D 110 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.32e-02 5.74e+03 6.18e+00 bond pdb=" N SER C 119 " pdb=" CA SER C 119 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" N SER C 185 " pdb=" CA SER C 185 " ideal model delta sigma weight residual 1.464 1.487 -0.024 1.25e-02 6.40e+03 3.57e+00 ... (remaining 4076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 5406 2.05 - 4.11: 118 4.11 - 6.16: 28 6.16 - 8.21: 2 8.21 - 10.27: 3 Bond angle restraints: 5557 Sorted by residual: angle pdb=" C SER C 179 " pdb=" N ASP C 180 " pdb=" CA ASP C 180 " ideal model delta sigma weight residual 122.07 127.27 -5.20 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C ALA C 137 " pdb=" N GLN C 138 " pdb=" CA GLN C 138 " ideal model delta sigma weight residual 122.07 127.19 -5.12 1.43e+00 4.89e-01 1.28e+01 angle pdb=" C ILE D 154 " pdb=" N ASP D 155 " pdb=" CA ASP D 155 " ideal model delta sigma weight residual 122.19 127.23 -5.04 1.41e+00 5.03e-01 1.28e+01 angle pdb=" C ASP D 174 " pdb=" N SER D 175 " pdb=" CA SER D 175 " ideal model delta sigma weight residual 122.19 127.16 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C ASN C 162 " pdb=" N SER C 163 " pdb=" CA SER C 163 " ideal model delta sigma weight residual 122.34 127.21 -4.87 1.39e+00 5.18e-01 1.23e+01 ... (remaining 5552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.81: 2296 11.81 - 23.62: 110 23.62 - 35.43: 33 35.43 - 47.24: 17 47.24 - 59.05: 1 Dihedral angle restraints: 2457 sinusoidal: 955 harmonic: 1502 Sorted by residual: dihedral pdb=" CA TRP C 195 " pdb=" C TRP C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR C 101 " pdb=" C TYR C 101 " pdb=" N ASP C 102 " pdb=" CA ASP C 102 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS A 535 " pdb=" C LYS A 535 " pdb=" N ASN A 536 " pdb=" CA ASN A 536 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 532 0.066 - 0.132: 79 0.132 - 0.199: 10 0.199 - 0.265: 2 0.265 - 0.331: 2 Chirality restraints: 625 Sorted by residual: chirality pdb=" CB ILE D 121 " pdb=" CA ILE D 121 " pdb=" CG1 ILE D 121 " pdb=" CG2 ILE D 121 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL C 188 " pdb=" CA VAL C 188 " pdb=" CG1 VAL C 188 " pdb=" CG2 VAL C 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL C 204 " pdb=" CA VAL C 204 " pdb=" CG1 VAL C 204 " pdb=" CG2 VAL C 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 622 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 118 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C VAL C 118 " -0.071 2.00e-02 2.50e+03 pdb=" O VAL C 118 " 0.027 2.00e-02 2.50e+03 pdb=" N SER C 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 195 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO C 196 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 204 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C VAL C 204 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 204 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 205 " 0.014 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 749 2.79 - 3.32: 3126 3.32 - 3.84: 6244 3.84 - 4.37: 6603 4.37 - 4.90: 11958 Nonbonded interactions: 28680 Sorted by model distance: nonbonded pdb=" OG SER D 22 " pdb=" OD1 ASP D 74 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASN C 61 " pdb=" N GLN C 62 " model vdw 2.374 3.120 nonbonded pdb=" O PRO C 7 " pdb=" OG1 THR C 114 " model vdw 2.393 3.040 nonbonded pdb=" OG SER D 205 " pdb=" O SER D 207 " model vdw 2.396 3.040 nonbonded pdb=" O ALA C 105 " pdb=" OG SER D 95 " model vdw 2.403 3.040 ... (remaining 28675 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 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.010 Find NCS groups from input model: 0.040 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.004 0.054 4081 Z= 0.264 Angle : 0.743 10.268 5557 Z= 0.419 Chirality : 0.054 0.331 625 Planarity : 0.006 0.070 712 Dihedral : 8.507 59.046 1472 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -1.34 (0.31), residues: 508 helix: -4.97 (0.38), residues: 8 sheet: -0.12 (0.30), residues: 220 loop : -1.41 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 39 HIS 0.002 0.001 HIS D 193 PHE 0.021 0.002 PHE D 143 TYR 0.014 0.001 TYR C 103 ARG 0.004 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.465 Fit side-chains REVERT: C 38 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (tttt) REVERT: C 61 ASN cc_start: 0.8783 (t0) cc_final: 0.8576 (t0) REVERT: C 63 LYS cc_start: 0.8882 (tttt) cc_final: 0.8569 (ttpp) REVERT: C 88 SER cc_start: 0.8757 (p) cc_final: 0.8480 (p) REVERT: C 91 SER cc_start: 0.8041 (m) cc_final: 0.7726 (p) REVERT: C 114 THR cc_start: 0.7706 (m) cc_final: 0.7418 (p) REVERT: C 144 THR cc_start: 0.8047 (m) cc_final: 0.7792 (m) REVERT: C 172 THR cc_start: 0.8640 (m) cc_final: 0.8403 (p) REVERT: C 193 SER cc_start: 0.7975 (p) cc_final: 0.7677 (p) REVERT: D 37 MET cc_start: 0.7757 (tpp) cc_final: 0.6524 (tpp) REVERT: D 86 ASP cc_start: 0.8105 (m-30) cc_final: 0.7819 (m-30) REVERT: D 215 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8179 (ttp80) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1725 time to fit residues: 20.2351 Evaluate side-chains 81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 178 GLN D 6 GLN D 42 GLN B 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.084144 restraints weight = 7158.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.086187 restraints weight = 4131.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087534 restraints weight = 2807.118| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4081 Z= 0.339 Angle : 0.621 5.024 5557 Z= 0.325 Chirality : 0.045 0.151 625 Planarity : 0.005 0.044 712 Dihedral : 4.513 23.429 551 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.97 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 5.54 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.34), residues: 508 helix: -2.93 (1.45), residues: 7 sheet: 0.33 (0.32), residues: 221 loop : -0.88 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 39 HIS 0.008 0.003 HIS D 193 PHE 0.017 0.002 PHE C 153 TYR 0.013 0.002 TYR D 53 ARG 0.006 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.416 Fit side-chains REVERT: C 63 LYS cc_start: 0.8810 (tttt) cc_final: 0.8599 (ttpp) REVERT: C 91 SER cc_start: 0.8466 (m) cc_final: 0.8013 (p) REVERT: C 115 LEU cc_start: 0.8265 (tp) cc_final: 0.7982 (tt) REVERT: C 193 SER cc_start: 0.8222 (p) cc_final: 0.8014 (p) REVERT: C 204 VAL cc_start: 0.8088 (p) cc_final: 0.7732 (m) REVERT: C 215 LYS cc_start: 0.7352 (mmmt) cc_final: 0.6495 (mmmt) REVERT: D 29 VAL cc_start: 0.8398 (m) cc_final: 0.8072 (p) REVERT: D 37 MET cc_start: 0.7725 (tpp) cc_final: 0.7354 (mmm) REVERT: D 86 ASP cc_start: 0.8289 (m-30) cc_final: 0.7982 (m-30) REVERT: D 215 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8260 (ttp80) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 0.1469 time to fit residues: 18.2806 Evaluate side-chains 96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 1 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 6 GLN A 532 ASN A 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.081878 restraints weight = 7114.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.083843 restraints weight = 4138.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.085138 restraints weight = 2839.164| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4081 Z= 0.306 Angle : 0.589 5.999 5557 Z= 0.303 Chirality : 0.044 0.136 625 Planarity : 0.004 0.035 712 Dihedral : 4.459 24.980 551 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.36 % Favored : 97.44 % Rotamer: Outliers : 2.44 % Allowed : 7.76 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.34), residues: 508 helix: -2.60 (1.62), residues: 8 sheet: 0.71 (0.34), residues: 209 loop : -0.78 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 39 HIS 0.005 0.002 HIS D 80 PHE 0.011 0.002 PHE C 153 TYR 0.013 0.002 TYR C 80 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.472 Fit side-chains REVERT: C 63 LYS cc_start: 0.8837 (tttt) cc_final: 0.8555 (ttpp) REVERT: C 91 SER cc_start: 0.8561 (m) cc_final: 0.8101 (p) REVERT: C 193 SER cc_start: 0.8231 (p) cc_final: 0.8027 (p) REVERT: C 204 VAL cc_start: 0.8277 (p) cc_final: 0.7955 (m) REVERT: C 215 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6399 (mmmt) REVERT: D 37 MET cc_start: 0.7738 (tpp) cc_final: 0.7374 (mmm) REVERT: D 86 ASP cc_start: 0.8276 (m-30) cc_final: 0.7928 (m-30) REVERT: D 215 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8339 (ttp80) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.1703 time to fit residues: 18.2977 Evaluate side-chains 84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain A residue 571 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 2 optimal weight: 0.0370 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.081335 restraints weight = 7185.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.083350 restraints weight = 4149.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.084712 restraints weight = 2792.928| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4081 Z= 0.219 Angle : 0.537 5.402 5557 Z= 0.274 Chirality : 0.043 0.136 625 Planarity : 0.004 0.032 712 Dihedral : 4.204 23.600 551 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 10.42 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.01 (0.36), residues: 508 helix: -2.14 (1.83), residues: 8 sheet: 0.78 (0.34), residues: 217 loop : -0.56 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 39 HIS 0.003 0.001 HIS D 202 PHE 0.008 0.001 PHE A 559 TYR 0.008 0.001 TYR C 80 ARG 0.001 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.419 Fit side-chains REVERT: C 91 SER cc_start: 0.8595 (m) cc_final: 0.8135 (p) REVERT: C 193 SER cc_start: 0.8292 (p) cc_final: 0.8076 (p) REVERT: C 204 VAL cc_start: 0.8284 (p) cc_final: 0.7993 (m) REVERT: C 215 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6501 (mmmt) REVERT: D 37 MET cc_start: 0.7686 (tpp) cc_final: 0.7133 (tmm) REVERT: D 86 ASP cc_start: 0.8301 (m-30) cc_final: 0.7952 (m-30) REVERT: D 152 TRP cc_start: 0.8817 (m100) cc_final: 0.8151 (m100) REVERT: D 215 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8336 (ttp80) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.1713 time to fit residues: 16.5368 Evaluate side-chains 81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.0040 chunk 25 optimal weight: 0.0270 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 6 GLN A 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.089979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.078769 restraints weight = 7440.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.080799 restraints weight = 4228.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.082105 restraints weight = 2822.068| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 4081 Z= 0.348 Angle : 0.609 7.448 5557 Z= 0.313 Chirality : 0.044 0.144 625 Planarity : 0.004 0.031 712 Dihedral : 4.527 22.830 551 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 2.66 % Allowed : 10.20 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -0.02 (0.35), residues: 508 helix: -1.95 (1.87), residues: 8 sheet: 0.95 (0.34), residues: 214 loop : -0.72 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 106 HIS 0.006 0.002 HIS D 80 PHE 0.013 0.002 PHE C 153 TYR 0.011 0.002 TYR C 80 ARG 0.003 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.440 Fit side-chains REVERT: C 91 SER cc_start: 0.8691 (m) cc_final: 0.8234 (p) REVERT: C 193 SER cc_start: 0.8194 (p) cc_final: 0.7989 (p) REVERT: C 204 VAL cc_start: 0.8376 (p) cc_final: 0.8077 (m) REVERT: C 215 LYS cc_start: 0.7484 (mmmt) cc_final: 0.6678 (mmmt) REVERT: D 1 ASP cc_start: 0.8449 (p0) cc_final: 0.8158 (p0) REVERT: D 32 SER cc_start: 0.8747 (m) cc_final: 0.8379 (p) REVERT: D 37 MET cc_start: 0.7653 (tpp) cc_final: 0.7112 (tmm) REVERT: D 86 ASP cc_start: 0.8331 (m-30) cc_final: 0.7991 (m-30) REVERT: D 152 TRP cc_start: 0.8832 (m100) cc_final: 0.8106 (m100) REVERT: D 215 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8333 (ttp80) outliers start: 12 outliers final: 12 residues processed: 79 average time/residue: 0.1756 time to fit residues: 17.1424 Evaluate side-chains 83 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN A 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.080368 restraints weight = 7267.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.082396 restraints weight = 4164.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.083736 restraints weight = 2784.926| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4081 Z= 0.185 Angle : 0.527 6.399 5557 Z= 0.267 Chirality : 0.042 0.136 625 Planarity : 0.003 0.031 712 Dihedral : 4.204 23.700 551 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.15 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 11.09 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.14 (0.36), residues: 508 helix: -1.58 (1.97), residues: 8 sheet: 0.95 (0.34), residues: 220 loop : -0.55 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 39 HIS 0.003 0.001 HIS D 202 PHE 0.006 0.001 PHE D 102 TYR 0.007 0.001 TYR D 53 ARG 0.002 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.454 Fit side-chains REVERT: C 91 SER cc_start: 0.8690 (m) cc_final: 0.8240 (p) REVERT: C 193 SER cc_start: 0.8269 (p) cc_final: 0.8064 (p) REVERT: C 204 VAL cc_start: 0.8301 (p) cc_final: 0.8045 (m) REVERT: C 215 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6565 (mmmt) REVERT: D 1 ASP cc_start: 0.8425 (p0) cc_final: 0.8102 (p0) REVERT: D 32 SER cc_start: 0.8759 (m) cc_final: 0.8387 (p) REVERT: D 37 MET cc_start: 0.7612 (tpp) cc_final: 0.7126 (tmm) REVERT: D 86 ASP cc_start: 0.8346 (m-30) cc_final: 0.7985 (m-30) REVERT: D 152 TRP cc_start: 0.8814 (m100) cc_final: 0.8152 (m100) REVERT: D 215 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8317 (ttp80) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1613 time to fit residues: 16.4185 Evaluate side-chains 80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 29 optimal weight: 0.0070 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.080564 restraints weight = 7359.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.082607 restraints weight = 4193.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.083970 restraints weight = 2797.815| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4081 Z= 0.169 Angle : 0.506 5.650 5557 Z= 0.256 Chirality : 0.042 0.155 625 Planarity : 0.003 0.032 712 Dihedral : 4.065 24.220 551 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 2.22 % Allowed : 10.86 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.37), residues: 508 helix: -1.18 (2.12), residues: 8 sheet: 1.02 (0.34), residues: 220 loop : -0.47 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 39 HIS 0.002 0.001 HIS D 202 PHE 0.008 0.001 PHE D 102 TYR 0.007 0.001 TYR D 53 ARG 0.001 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.410 Fit side-chains REVERT: C 91 SER cc_start: 0.8693 (m) cc_final: 0.8254 (p) REVERT: C 193 SER cc_start: 0.8287 (p) cc_final: 0.8084 (p) REVERT: C 204 VAL cc_start: 0.8271 (p) cc_final: 0.8032 (m) REVERT: C 215 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6451 (mmmt) REVERT: D 1 ASP cc_start: 0.8449 (p0) cc_final: 0.8136 (p0) REVERT: D 32 SER cc_start: 0.8759 (m) cc_final: 0.8393 (p) REVERT: D 37 MET cc_start: 0.7613 (tpp) cc_final: 0.7106 (tmm) REVERT: D 86 ASP cc_start: 0.8362 (m-30) cc_final: 0.7979 (m-30) REVERT: D 152 TRP cc_start: 0.8821 (m100) cc_final: 0.8145 (m100) REVERT: D 213 PHE cc_start: 0.8774 (p90) cc_final: 0.8456 (p90) REVERT: D 215 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8288 (ttp80) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.1626 time to fit residues: 16.0488 Evaluate side-chains 80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.0170 chunk 21 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.0040 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.0886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 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 = 0.3032 r_free = 0.3032 target = 0.092932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.081747 restraints weight = 7231.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.083782 restraints weight = 4137.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085125 restraints weight = 2778.631| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4081 Z= 0.120 Angle : 0.476 5.405 5557 Z= 0.241 Chirality : 0.042 0.148 625 Planarity : 0.004 0.041 712 Dihedral : 3.897 26.405 551 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 2.22 % Allowed : 11.31 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.45 (0.38), residues: 508 helix: -0.80 (2.29), residues: 8 sheet: 1.10 (0.34), residues: 222 loop : -0.32 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 39 HIS 0.001 0.001 HIS D 193 PHE 0.006 0.001 PHE D 102 TYR 0.006 0.001 TYR D 53 ARG 0.001 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.437 Fit side-chains REVERT: C 39 GLN cc_start: 0.7294 (tt0) cc_final: 0.6972 (mt0) REVERT: C 91 SER cc_start: 0.8682 (m) cc_final: 0.8257 (p) REVERT: C 157 VAL cc_start: 0.8041 (m) cc_final: 0.7809 (p) REVERT: C 193 SER cc_start: 0.8263 (p) cc_final: 0.8048 (p) REVERT: C 215 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6491 (mmmt) REVERT: D 1 ASP cc_start: 0.8420 (p0) cc_final: 0.8094 (p0) REVERT: D 32 SER cc_start: 0.8771 (m) cc_final: 0.8408 (p) REVERT: D 37 MET cc_start: 0.7612 (tpp) cc_final: 0.7093 (tmm) REVERT: D 86 ASP cc_start: 0.8373 (m-30) cc_final: 0.7992 (m-30) REVERT: D 152 TRP cc_start: 0.8794 (m100) cc_final: 0.8256 (m100) REVERT: D 186 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8708 (m) REVERT: D 213 PHE cc_start: 0.8739 (p90) cc_final: 0.8429 (p90) REVERT: D 215 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8300 (ttp80) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.1725 time to fit residues: 17.8108 Evaluate side-chains 80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.0370 chunk 46 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 chunk 23 optimal weight: 0.1980 chunk 16 optimal weight: 0.0050 overall best weight: 0.0446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.082908 restraints weight = 7349.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084940 restraints weight = 4189.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.086275 restraints weight = 2824.570| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4081 Z= 0.110 Angle : 0.467 5.354 5557 Z= 0.236 Chirality : 0.042 0.159 625 Planarity : 0.004 0.036 712 Dihedral : 3.816 27.667 551 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.15 % Favored : 96.65 % Rotamer: Outliers : 1.77 % Allowed : 11.75 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.38), residues: 508 helix: -0.58 (2.39), residues: 8 sheet: 1.12 (0.34), residues: 222 loop : -0.19 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 39 HIS 0.001 0.000 HIS D 193 PHE 0.005 0.001 PHE D 102 TYR 0.006 0.001 TYR D 53 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.433 Fit side-chains REVERT: C 39 GLN cc_start: 0.7204 (tt0) cc_final: 0.7000 (mt0) REVERT: C 91 SER cc_start: 0.8632 (m) cc_final: 0.8234 (p) REVERT: C 157 VAL cc_start: 0.7934 (m) cc_final: 0.7659 (p) REVERT: C 193 SER cc_start: 0.8225 (p) cc_final: 0.7990 (p) REVERT: D 32 SER cc_start: 0.8743 (m) cc_final: 0.8415 (p) REVERT: D 37 MET cc_start: 0.7560 (tpp) cc_final: 0.7099 (tmm) REVERT: D 86 ASP cc_start: 0.8369 (m-30) cc_final: 0.8060 (m-30) REVERT: D 152 TRP cc_start: 0.8758 (m100) cc_final: 0.8290 (m100) REVERT: D 186 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8535 (m) REVERT: D 213 PHE cc_start: 0.8711 (p90) cc_final: 0.8372 (p90) REVERT: D 215 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8338 (ttp80) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1611 time to fit residues: 15.1119 Evaluate side-chains 77 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.089414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.078411 restraints weight = 7467.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.080356 restraints weight = 4209.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.081681 restraints weight = 2831.161| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4081 Z= 0.339 Angle : 0.602 6.133 5557 Z= 0.309 Chirality : 0.044 0.153 625 Planarity : 0.004 0.041 712 Dihedral : 4.338 21.603 551 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 1.77 % Allowed : 11.53 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.33 (0.37), residues: 508 helix: -0.81 (2.29), residues: 8 sheet: 1.06 (0.34), residues: 221 loop : -0.44 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 106 HIS 0.007 0.002 HIS D 80 PHE 0.011 0.002 PHE C 153 TYR 0.013 0.002 TYR C 80 ARG 0.007 0.001 ARG A 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.444 Fit side-chains REVERT: C 91 SER cc_start: 0.8675 (m) cc_final: 0.8248 (p) REVERT: C 193 SER cc_start: 0.8202 (p) cc_final: 0.7985 (p) REVERT: C 215 LYS cc_start: 0.7493 (mmmt) cc_final: 0.6692 (mmmt) REVERT: D 1 ASP cc_start: 0.8448 (p0) cc_final: 0.8129 (p0) REVERT: D 32 SER cc_start: 0.8774 (m) cc_final: 0.8456 (p) REVERT: D 37 MET cc_start: 0.7640 (tpp) cc_final: 0.7190 (tmm) REVERT: D 86 ASP cc_start: 0.8374 (m-30) cc_final: 0.8014 (m-30) REVERT: D 152 TRP cc_start: 0.8857 (m100) cc_final: 0.8125 (m100) REVERT: D 213 PHE cc_start: 0.8779 (p90) cc_final: 0.8487 (p90) REVERT: D 215 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8316 (ttp80) outliers start: 8 outliers final: 8 residues processed: 93 average time/residue: 0.1543 time to fit residues: 18.2616 Evaluate side-chains 88 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain A residue 592 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.0970 chunk 33 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 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 = 0.2987 r_free = 0.2987 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.079437 restraints weight = 7241.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.081361 restraints weight = 4106.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.082645 restraints weight = 2786.807| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4081 Z= 0.194 Angle : 0.573 7.296 5557 Z= 0.279 Chirality : 0.043 0.156 625 Planarity : 0.004 0.040 712 Dihedral : 4.218 23.525 551 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Rotamer: Outliers : 2.00 % Allowed : 12.64 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.36 (0.37), residues: 508 helix: -0.65 (2.35), residues: 8 sheet: 1.08 (0.34), residues: 220 loop : -0.41 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 39 HIS 0.003 0.001 HIS D 202 PHE 0.006 0.001 PHE A 559 TYR 0.008 0.001 TYR C 80 ARG 0.002 0.000 ARG A 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.27 seconds wall clock time: 32 minutes 8.06 seconds (1928.06 seconds total)