Starting phenix.real_space_refine on Tue Feb 13 04:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/02_2024/8g4e_29718_updated.pdb" } resolution = 2.98 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= 0.013 sd= 0.081 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 7 5.16 5 C 1957 2.51 5 N 543 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3097 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 163} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1826 Unusual residues: {'CRO': 1} Classifications: {'peptide': 228, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216, None: 2} Not linked: pdbres="LEU B 64 " pdbres="CRO B 66 " Not linked: pdbres="CRO B 66 " pdbres="VAL B 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.75 Number of scatterers: 3097 At special positions: 0 Unit cell: (66.825, 77.9625, 66.825, 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 7 16.00 O 590 8.00 N 543 7.00 C 1957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 566.8 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 1 sheets defined 30.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 156 through 177 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.665A pdb=" N ARG A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 83 through 86 No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing sheet with id= A, first strand: chain 'B' and resid 25 through 36 removed outlier: 6.079A pdb=" N LEU B 119 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 17 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 121 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASP B 19 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 123 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASP B 21 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 125 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 164 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B 151 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 219 " --> pdb=" O SER B 208 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 402 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: 0.79 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1048 1.34 - 1.46: 444 1.46 - 1.57: 1654 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3158 Sorted by residual: bond pdb=" C MET B 88 " pdb=" N PRO B 89 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.44e-02 4.82e+03 5.39e+00 bond pdb=" C1 CRO B 66 " pdb=" N2 CRO B 66 " ideal model delta sigma weight residual 1.289 1.328 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" CZ CRO B 66 " pdb=" OH CRO B 66 " ideal model delta sigma weight residual 1.341 1.373 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CA1 CRO B 66 " pdb=" N1 CRO B 66 " ideal model delta sigma weight residual 1.448 1.475 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C3 CRO B 66 " pdb=" CA3 CRO B 66 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.11e+00 ... (remaining 3153 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.25: 106 107.25 - 113.92: 1795 113.92 - 120.59: 1191 120.59 - 127.26: 1146 127.26 - 133.93: 40 Bond angle restraints: 4278 Sorted by residual: angle pdb=" N GLY B 33 " pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 111.08 115.61 -4.53 1.62e+00 3.81e-01 7.83e+00 angle pdb=" N MET B 88 " pdb=" CA MET B 88 " pdb=" C MET B 88 " ideal model delta sigma weight residual 109.81 114.80 -4.99 2.21e+00 2.05e-01 5.09e+00 angle pdb=" C ASP B 129 " pdb=" CA ASP B 129 " pdb=" CB ASP B 129 " ideal model delta sigma weight residual 111.26 108.23 3.03 1.67e+00 3.59e-01 3.29e+00 angle pdb=" C ILE B 128 " pdb=" N ASP B 129 " pdb=" CA ASP B 129 " ideal model delta sigma weight residual 123.47 126.22 -2.75 1.53e+00 4.27e-01 3.24e+00 angle pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" N TYR A 179 " ideal model delta sigma weight residual 118.50 116.80 1.70 9.90e-01 1.02e+00 2.95e+00 ... (remaining 4273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1649 17.53 - 35.06: 162 35.06 - 52.60: 47 52.60 - 70.13: 13 70.13 - 87.66: 3 Dihedral angle restraints: 1874 sinusoidal: 746 harmonic: 1128 Sorted by residual: dihedral pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " pdb=" CD GLU B 111 " pdb=" OE1 GLU B 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.66 -87.66 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASN B 23 " pdb=" CB ASN B 23 " pdb=" CG ASN B 23 " pdb=" OD1 ASN B 23 " ideal model delta sinusoidal sigma weight residual -90.00 -156.78 66.78 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG A 176 " pdb=" CD ARG A 176 " pdb=" NE ARG A 176 " pdb=" CZ ARG A 176 " ideal model delta sinusoidal sigma weight residual 180.00 -136.68 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 1871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 239 0.023 - 0.046: 139 0.046 - 0.069: 56 0.069 - 0.092: 23 0.092 - 0.115: 22 Chirality restraints: 479 Sorted by residual: chirality pdb=" CB1 CRO B 66 " pdb=" CG1 CRO B 66 " pdb=" OG1 CRO B 66 " pdb=" CA1 CRO B 66 " both_signs ideal model delta sigma weight residual False -2.35 -2.47 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE B 47 " pdb=" N ILE B 47 " pdb=" C ILE B 47 " pdb=" CB ILE B 47 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 476 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO B 66 " -0.008 2.00e-02 2.50e+03 3.30e-02 2.72e+01 pdb=" CG2 CRO B 66 " -0.046 2.00e-02 2.50e+03 pdb=" C1 CRO B 66 " 0.017 2.00e-02 2.50e+03 pdb=" C2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" CA1 CRO B 66 " 0.012 2.00e-02 2.50e+03 pdb=" CA2 CRO B 66 " 0.014 2.00e-02 2.50e+03 pdb=" CA3 CRO B 66 " -0.069 2.00e-02 2.50e+03 pdb=" N2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" N3 CRO B 66 " -0.014 2.00e-02 2.50e+03 pdb=" O2 CRO B 66 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 269 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 236 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 706 2.79 - 3.32: 2604 3.32 - 3.85: 4879 3.85 - 4.37: 5852 4.37 - 4.90: 10430 Nonbonded interactions: 24471 Sorted by model distance: nonbonded pdb=" NE2 GLN B 183 " pdb=" OD1 ASN B 185 " model vdw 2.266 2.520 nonbonded pdb=" N ASP A 230 " pdb=" OD1 ASP A 230 " model vdw 2.330 2.520 nonbonded pdb=" OG1 THR A 202 " pdb=" ND1 HIS A 205 " model vdw 2.333 2.520 nonbonded pdb=" O PRO B 56 " pdb=" OG1 THR B 59 " model vdw 2.339 2.440 nonbonded pdb=" NZ LYS A 162 " pdb=" OE2 GLU A 166 " model vdw 2.378 2.520 ... (remaining 24466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.880 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: 3.600 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.039 3158 Z= 0.180 Angle : 0.528 4.986 4278 Z= 0.293 Chirality : 0.040 0.115 479 Planarity : 0.004 0.041 559 Dihedral : 15.966 87.661 1148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.16 % Allowed : 16.67 % Favored : 81.17 % 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 (0.44), residues: 390 helix: 1.08 (0.45), residues: 137 sheet: 0.57 (0.50), residues: 121 loop : -0.75 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.376 Fit side-chains REVERT: A 293 ASN cc_start: 0.7980 (m-40) cc_final: 0.7628 (m110) REVERT: B 34 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7799 (mt-10) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 1.3233 time to fit residues: 81.4680 Evaluate side-chains 44 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 0.0050 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 23 ASN B 77 HIS B 81 HIS B 217 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3158 Z= 0.182 Angle : 0.499 5.146 4278 Z= 0.259 Chirality : 0.042 0.124 479 Planarity : 0.004 0.043 559 Dihedral : 6.894 71.880 433 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.48 % Allowed : 18.52 % Favored : 75.00 % 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: 0.58 (0.43), residues: 390 helix: 1.07 (0.44), residues: 139 sheet: 0.89 (0.50), residues: 117 loop : -0.74 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.009 0.001 PHE A 298 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6610 (mpt-90) REVERT: A 291 ASP cc_start: 0.7857 (t0) cc_final: 0.7650 (t0) REVERT: B 34 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7730 (mt-10) outliers start: 21 outliers final: 13 residues processed: 51 average time/residue: 1.1956 time to fit residues: 62.8577 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3158 Z= 0.192 Angle : 0.496 5.480 4278 Z= 0.256 Chirality : 0.042 0.125 479 Planarity : 0.004 0.044 559 Dihedral : 6.005 71.236 426 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.10 % Allowed : 19.14 % Favored : 73.77 % 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: 0.68 (0.43), residues: 390 helix: 1.05 (0.44), residues: 139 sheet: 1.00 (0.50), residues: 117 loop : -0.60 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.010 0.002 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 37 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6668 (mpt-90) REVERT: A 291 ASP cc_start: 0.7895 (t0) cc_final: 0.7593 (t0) REVERT: A 301 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7903 (m) REVERT: B 5 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: B 34 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7823 (mt-10) outliers start: 23 outliers final: 12 residues processed: 50 average time/residue: 1.1920 time to fit residues: 61.4765 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3158 Z= 0.116 Angle : 0.465 6.630 4278 Z= 0.239 Chirality : 0.041 0.139 479 Planarity : 0.004 0.040 559 Dihedral : 5.728 73.070 424 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.86 % Allowed : 20.06 % Favored : 74.07 % 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: 0.98 (0.44), residues: 390 helix: 1.36 (0.45), residues: 139 sheet: 1.13 (0.50), residues: 117 loop : -0.48 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.006 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: A 291 ASP cc_start: 0.7810 (t0) cc_final: 0.7499 (t0) REVERT: A 301 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7889 (m) REVERT: B 5 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 34 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 214 LYS cc_start: 0.8438 (mttt) cc_final: 0.8212 (mttm) outliers start: 19 outliers final: 11 residues processed: 51 average time/residue: 1.1719 time to fit residues: 61.5596 Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3158 Z= 0.138 Angle : 0.471 6.964 4278 Z= 0.242 Chirality : 0.041 0.123 479 Planarity : 0.004 0.041 559 Dihedral : 5.652 72.697 424 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.48 % Allowed : 20.68 % Favored : 72.84 % 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: 0.98 (0.44), residues: 390 helix: 1.31 (0.44), residues: 139 sheet: 1.20 (0.50), residues: 117 loop : -0.48 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.003 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: A 301 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7896 (m) REVERT: A 313 ASP cc_start: 0.6907 (m-30) cc_final: 0.6588 (t0) REVERT: B 5 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 34 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7805 (mt-10) outliers start: 21 outliers final: 12 residues processed: 51 average time/residue: 1.1312 time to fit residues: 59.5933 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3158 Z= 0.151 Angle : 0.492 7.979 4278 Z= 0.253 Chirality : 0.042 0.126 479 Planarity : 0.004 0.042 559 Dihedral : 5.527 72.298 423 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.79 % Allowed : 20.99 % Favored : 72.22 % 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: 1.02 (0.44), residues: 390 helix: 1.25 (0.44), residues: 139 sheet: 1.24 (0.50), residues: 117 loop : -0.38 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 36 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: A 301 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7902 (m) REVERT: A 313 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6551 (t0) REVERT: B 5 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 34 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 22 outliers final: 12 residues processed: 49 average time/residue: 1.2114 time to fit residues: 61.1371 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3158 Z= 0.159 Angle : 0.510 9.329 4278 Z= 0.261 Chirality : 0.042 0.122 479 Planarity : 0.004 0.042 559 Dihedral : 5.509 72.021 423 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.86 % Allowed : 21.60 % Favored : 72.53 % 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: 1.03 (0.44), residues: 390 helix: 1.20 (0.44), residues: 139 sheet: 1.25 (0.51), residues: 117 loop : -0.31 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 35 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: A 301 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7897 (m) REVERT: B 5 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 34 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 19 outliers final: 14 residues processed: 46 average time/residue: 1.1586 time to fit residues: 54.9784 Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 35 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3158 Z= 0.230 Angle : 0.550 9.941 4278 Z= 0.280 Chirality : 0.044 0.132 479 Planarity : 0.004 0.045 559 Dihedral : 5.612 70.288 423 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.86 % Allowed : 21.91 % Favored : 72.22 % 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: 0.77 (0.44), residues: 390 helix: 0.80 (0.43), residues: 140 sheet: 1.24 (0.51), residues: 117 loop : -0.35 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.011 0.002 PHE A 298 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 301 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7870 (m) REVERT: B 5 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 34 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7835 (mt-10) outliers start: 19 outliers final: 14 residues processed: 47 average time/residue: 1.1850 time to fit residues: 57.4717 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3158 Z= 0.189 Angle : 0.534 10.630 4278 Z= 0.272 Chirality : 0.043 0.129 479 Planarity : 0.004 0.044 559 Dihedral : 5.598 71.211 423 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.94 % Allowed : 22.53 % Favored : 72.53 % 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: 0.79 (0.44), residues: 390 helix: 0.77 (0.43), residues: 140 sheet: 1.23 (0.51), residues: 117 loop : -0.28 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.398 Fit side-chains REVERT: A 301 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7848 (m) REVERT: B 5 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: B 6 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 34 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7779 (mt-10) outliers start: 16 outliers final: 13 residues processed: 44 average time/residue: 1.2124 time to fit residues: 55.0484 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3158 Z= 0.154 Angle : 0.513 10.962 4278 Z= 0.262 Chirality : 0.042 0.146 479 Planarity : 0.004 0.043 559 Dihedral : 5.569 72.134 423 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.94 % Allowed : 22.22 % Favored : 72.84 % 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: 0.89 (0.44), residues: 390 helix: 0.84 (0.44), residues: 140 sheet: 1.31 (0.51), residues: 117 loop : -0.21 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 301 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (m) REVERT: B 5 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 34 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 214 LYS cc_start: 0.8428 (mttt) cc_final: 0.8201 (mttm) outliers start: 16 outliers final: 12 residues processed: 45 average time/residue: 1.3344 time to fit residues: 61.7572 Evaluate side-chains 49 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.153080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122210 restraints weight = 3609.287| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.03 r_work: 0.3256 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3158 Z= 0.187 Angle : 0.533 10.964 4278 Z= 0.272 Chirality : 0.043 0.157 479 Planarity : 0.004 0.044 559 Dihedral : 5.575 71.429 423 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.94 % Allowed : 22.53 % Favored : 72.53 % 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: 0.84 (0.44), residues: 390 helix: 0.74 (0.43), residues: 140 sheet: 1.32 (0.51), residues: 117 loop : -0.22 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.003 0.000 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.63 seconds wall clock time: 32 minutes 14.24 seconds (1934.24 seconds total)