Starting phenix.real_space_refine on Sat Dec 28 02:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw5_15691/12_2024/8aw5_15691.cif" } resolution = 2.8 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= 0.004 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 9 5.49 5 S 21 5.16 5 C 4887 2.51 5 N 975 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "C" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.66, per 1000 atoms: 0.66 Number of scatterers: 7023 At special positions: 0 Unit cell: (88.56, 93.48, 72.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 21 16.00 P 9 15.00 O 1128 8.00 N 975 7.00 C 4887 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 - 3.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 986.2 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 33 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.801A pdb=" N GLU A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 126 Processing helix chain 'A' and resid 133 through 167 removed outlier: 3.642A pdb=" N LEU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 200 Processing helix chain 'A' and resid 203 through 231 removed outlier: 4.082A pdb=" N GLY A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 256 Processing helix chain 'A' and resid 259 through 287 Proline residue: A 283 - end of helix Processing helix chain 'B' and resid 11 through 33 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.800A pdb=" N GLU B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 Processing helix chain 'B' and resid 133 through 167 removed outlier: 3.643A pdb=" N LEU B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 200 Processing helix chain 'B' and resid 203 through 231 removed outlier: 4.081A pdb=" N GLY B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 Processing helix chain 'B' and resid 259 through 287 Proline residue: B 283 - end of helix Processing helix chain 'C' and resid 11 through 33 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 74 through 101 removed outlier: 3.800A pdb=" N GLU C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 126 Processing helix chain 'C' and resid 133 through 167 removed outlier: 3.642A pdb=" N LEU C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 200 Processing helix chain 'C' and resid 203 through 231 removed outlier: 4.081A pdb=" N GLY C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 Processing helix chain 'C' and resid 259 through 287 Proline residue: C 283 - end of helix 523 hydrogen bonds defined for protein. 1551 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: 2.08 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 2444 1.38 - 1.55: 4708 1.55 - 1.72: 21 1.72 - 1.89: 36 1.89 - 2.06: 12 Bond restraints: 7221 Sorted by residual: bond pdb=" C21 POV C 404 " pdb=" O22 POV C 404 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C21 POV A 402 " pdb=" O22 POV A 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV B 402 " pdb=" O22 POV B 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV A 404 " pdb=" O22 POV A 404 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C21 POV A 403 " pdb=" O22 POV A 403 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9472 3.45 - 6.90: 219 6.90 - 10.35: 29 10.35 - 13.80: 24 13.80 - 17.25: 48 Bond angle restraints: 9792 Sorted by residual: angle pdb=" N GLU C 204 " pdb=" CA GLU C 204 " pdb=" C GLU C 204 " ideal model delta sigma weight residual 111.69 99.00 12.69 1.23e+00 6.61e-01 1.07e+02 angle pdb=" N GLU A 204 " pdb=" CA GLU A 204 " pdb=" C GLU A 204 " ideal model delta sigma weight residual 111.69 99.01 12.68 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N GLU B 204 " pdb=" CA GLU B 204 " pdb=" C GLU B 204 " ideal model delta sigma weight residual 112.45 98.98 13.47 1.39e+00 5.18e-01 9.39e+01 angle pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" C VAL C 32 " ideal model delta sigma weight residual 111.45 103.72 7.73 9.30e-01 1.16e+00 6.92e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 111.45 103.73 7.72 9.30e-01 1.16e+00 6.89e+01 ... (remaining 9787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 3951 28.36 - 56.72: 150 56.72 - 85.07: 45 85.07 - 113.43: 18 113.43 - 141.79: 6 Dihedral angle restraints: 4170 sinusoidal: 1827 harmonic: 2343 Sorted by residual: dihedral pdb=" C3 POV C 404 " pdb=" C31 POV C 404 " pdb=" O31 POV C 404 " pdb=" C32 POV C 404 " ideal model delta sinusoidal sigma weight residual 172.61 -45.60 -141.79 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV A 402 " pdb=" C31 POV A 402 " pdb=" O31 POV A 402 " pdb=" C32 POV A 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.64 -141.75 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV B 402 " pdb=" C31 POV B 402 " pdb=" O31 POV B 402 " pdb=" C32 POV B 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.67 -141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 779 0.062 - 0.123: 235 0.123 - 0.185: 65 0.185 - 0.247: 10 0.247 - 0.309: 12 Chirality restraints: 1101 Sorted by residual: chirality pdb=" CA GLU A 204 " pdb=" N GLU A 204 " pdb=" C GLU A 204 " pdb=" CB GLU A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU B 204 " pdb=" N GLU B 204 " pdb=" C GLU B 204 " pdb=" CB GLU B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU C 204 " pdb=" N GLU C 204 " pdb=" C GLU C 204 " pdb=" CB GLU C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1098 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 402 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C29 POV C 402 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV C 402 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV C 402 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 403 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV A 403 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV A 403 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV A 403 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 403 " 0.150 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV B 403 " -0.352 2.00e-02 2.50e+03 pdb="C210 POV B 403 " 0.354 2.00e-02 2.50e+03 pdb="C211 POV B 403 " -0.152 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2862 2.92 - 3.42: 7633 3.42 - 3.91: 12228 3.91 - 4.41: 13913 4.41 - 4.90: 22736 Nonbonded interactions: 59372 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" OH TYR A 184 " model vdw 2.427 3.040 nonbonded pdb=" OG SER B 157 " pdb=" OH TYR B 184 " model vdw 2.427 3.040 nonbonded pdb=" OG SER C 157 " pdb=" OH TYR C 184 " model vdw 2.428 3.040 nonbonded pdb=" O GLY B 29 " pdb=" OG1 THR B 33 " model vdw 2.446 3.040 nonbonded pdb=" O GLY A 29 " pdb=" OG1 THR A 33 " model vdw 2.446 3.040 ... (remaining 59367 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.820 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.017 0.233 7221 Z= 0.943 Angle : 1.758 17.246 9792 Z= 0.905 Chirality : 0.070 0.309 1101 Planarity : 0.036 0.272 1095 Dihedral : 18.375 141.787 2676 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.58 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 6.06 % Favored : 93.51 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 786 helix: 1.25 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -3.62 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 276 HIS 0.002 0.001 HIS C 81 PHE 0.014 0.002 PHE A 272 TYR 0.010 0.001 TYR B 164 ARG 0.002 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.671 Fit side-chains REVERT: A 14 LEU cc_start: 0.8819 (mt) cc_final: 0.8500 (mt) REVERT: A 171 GLU cc_start: 0.8036 (mp0) cc_final: 0.7750 (mp0) REVERT: B 143 VAL cc_start: 0.8928 (t) cc_final: 0.8700 (t) REVERT: B 203 LEU cc_start: 0.8183 (tp) cc_final: 0.7942 (tp) REVERT: B 246 GLN cc_start: 0.9056 (tp40) cc_final: 0.8711 (tp40) REVERT: C 243 MET cc_start: 0.8768 (mmt) cc_final: 0.8409 (mmt) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 1.1369 time to fit residues: 213.8846 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS C 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7221 Z= 0.281 Angle : 0.672 12.934 9792 Z= 0.318 Chirality : 0.041 0.197 1101 Planarity : 0.004 0.045 1095 Dihedral : 19.676 133.384 1278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.46 % Allowed : 14.86 % Favored : 81.67 % 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: 2.23 (0.30), residues: 786 helix: 2.45 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.82 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.004 0.001 HIS B 213 PHE 0.016 0.002 PHE B 272 TYR 0.015 0.001 TYR C 199 ARG 0.001 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.754 Fit side-chains REVERT: A 14 LEU cc_start: 0.8700 (mt) cc_final: 0.8418 (mt) REVERT: A 171 GLU cc_start: 0.8049 (mp0) cc_final: 0.7795 (mp0) REVERT: A 172 ARG cc_start: 0.6391 (tpm170) cc_final: 0.6020 (tpp-160) REVERT: A 201 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7754 (mmtp) REVERT: B 172 ARG cc_start: 0.6447 (tpm170) cc_final: 0.6141 (tpp-160) REVERT: C 243 MET cc_start: 0.8914 (mmt) cc_final: 0.8554 (mmt) outliers start: 24 outliers final: 6 residues processed: 116 average time/residue: 1.4999 time to fit residues: 181.9309 Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 181 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS B 246 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7221 Z= 0.263 Angle : 0.625 13.273 9792 Z= 0.299 Chirality : 0.039 0.196 1101 Planarity : 0.004 0.043 1095 Dihedral : 18.678 130.198 1278 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.90 % Allowed : 14.43 % Favored : 81.67 % 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: 2.72 (0.30), residues: 786 helix: 2.80 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.005 0.001 HIS B 213 PHE 0.016 0.002 PHE B 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.775 Fit side-chains REVERT: A 14 LEU cc_start: 0.8693 (mt) cc_final: 0.8408 (mt) REVERT: A 171 GLU cc_start: 0.8121 (mp0) cc_final: 0.7843 (mp0) REVERT: A 172 ARG cc_start: 0.6539 (tpm170) cc_final: 0.6183 (tpp-160) REVERT: A 201 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7672 (mmtm) REVERT: A 258 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.6944 (t80) REVERT: B 143 VAL cc_start: 0.9067 (t) cc_final: 0.8839 (t) REVERT: B 172 ARG cc_start: 0.6601 (tpm170) cc_final: 0.6336 (tpp-160) REVERT: B 234 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: C 243 MET cc_start: 0.8880 (mmt) cc_final: 0.8603 (mmt) REVERT: C 258 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.6819 (t80) outliers start: 27 outliers final: 9 residues processed: 116 average time/residue: 1.3987 time to fit residues: 170.1744 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS B 246 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7221 Z= 0.244 Angle : 0.596 6.891 9792 Z= 0.288 Chirality : 0.038 0.135 1101 Planarity : 0.004 0.040 1095 Dihedral : 18.045 127.292 1278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.03 % Allowed : 15.30 % Favored : 81.67 % 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: 2.86 (0.30), residues: 786 helix: 2.88 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS C 213 PHE 0.015 0.002 PHE C 272 TYR 0.012 0.001 TYR C 199 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.848 Fit side-chains REVERT: A 14 LEU cc_start: 0.8699 (mt) cc_final: 0.8422 (mt) REVERT: A 201 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7881 (mmtp) REVERT: A 258 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.6947 (t80) REVERT: B 143 VAL cc_start: 0.9061 (t) cc_final: 0.8853 (t) REVERT: B 172 ARG cc_start: 0.6507 (tpm170) cc_final: 0.6199 (tpp-160) REVERT: B 234 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: C 78 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7318 (tp30) REVERT: C 243 MET cc_start: 0.8868 (mmt) cc_final: 0.8606 (mmt) REVERT: C 258 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.6791 (t80) outliers start: 21 outliers final: 7 residues processed: 104 average time/residue: 1.4999 time to fit residues: 163.3479 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS B 141 HIS C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7221 Z= 0.230 Angle : 0.585 6.544 9792 Z= 0.283 Chirality : 0.038 0.132 1101 Planarity : 0.004 0.041 1095 Dihedral : 17.632 126.272 1278 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.46 % Allowed : 15.44 % Favored : 81.10 % 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: 2.92 (0.30), residues: 786 helix: 2.93 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.53 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS B 213 PHE 0.014 0.002 PHE C 272 TYR 0.013 0.001 TYR C 199 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.718 Fit side-chains REVERT: A 14 LEU cc_start: 0.8735 (mt) cc_final: 0.8462 (mt) REVERT: A 78 GLU cc_start: 0.7546 (tp30) cc_final: 0.7342 (tp30) REVERT: A 171 GLU cc_start: 0.8197 (mp0) cc_final: 0.7819 (mp0) REVERT: A 258 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6853 (t80) REVERT: B 143 VAL cc_start: 0.9059 (t) cc_final: 0.8847 (t) REVERT: B 172 ARG cc_start: 0.6492 (tpm170) cc_final: 0.6013 (mmp80) REVERT: B 201 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7875 (mmtm) REVERT: B 234 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8128 (ptmm) REVERT: C 78 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7207 (tp30) REVERT: C 243 MET cc_start: 0.8823 (mmt) cc_final: 0.8567 (mmt) REVERT: C 258 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6713 (t80) outliers start: 24 outliers final: 9 residues processed: 112 average time/residue: 1.4418 time to fit residues: 169.1795 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7221 Z= 0.259 Angle : 0.607 6.728 9792 Z= 0.293 Chirality : 0.039 0.137 1101 Planarity : 0.004 0.042 1095 Dihedral : 17.645 127.645 1278 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.05 % Favored : 96.69 % Rotamer: Outliers : 3.46 % Allowed : 15.73 % Favored : 80.81 % 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: 2.84 (0.30), residues: 786 helix: 2.87 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 276 HIS 0.003 0.001 HIS B 213 PHE 0.016 0.002 PHE C 272 TYR 0.014 0.001 TYR C 199 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.759 Fit side-chains REVERT: A 14 LEU cc_start: 0.8751 (mt) cc_final: 0.8464 (mt) REVERT: A 172 ARG cc_start: 0.7114 (mmp-170) cc_final: 0.6703 (mmp80) REVERT: A 258 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 287 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7986 (ptpp) REVERT: B 143 VAL cc_start: 0.9076 (t) cc_final: 0.8852 (t) REVERT: B 172 ARG cc_start: 0.6596 (tpm170) cc_final: 0.6109 (mmp80) REVERT: B 201 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7888 (mmtm) REVERT: B 234 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8135 (ptmm) REVERT: C 78 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7204 (tp30) REVERT: C 243 MET cc_start: 0.8855 (mmt) cc_final: 0.8590 (mmt) REVERT: C 258 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6666 (t80) outliers start: 24 outliers final: 12 residues processed: 113 average time/residue: 1.4735 time to fit residues: 174.0790 Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS B 141 HIS C 74 GLN C 141 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7221 Z= 0.212 Angle : 0.584 6.507 9792 Z= 0.284 Chirality : 0.037 0.127 1101 Planarity : 0.004 0.039 1095 Dihedral : 17.132 121.834 1278 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.54 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 16.74 % Favored : 80.23 % 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: 2.96 (0.30), residues: 786 helix: 2.96 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.52 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.002 0.001 HIS C 213 PHE 0.013 0.001 PHE C 272 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.759 Fit side-chains REVERT: A 14 LEU cc_start: 0.8707 (mt) cc_final: 0.8446 (mt) REVERT: A 171 GLU cc_start: 0.8213 (mp0) cc_final: 0.7928 (mp0) REVERT: A 258 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6550 (t80) REVERT: B 143 VAL cc_start: 0.8984 (t) cc_final: 0.8783 (t) REVERT: B 172 ARG cc_start: 0.6580 (tpm170) cc_final: 0.6135 (mmp80) REVERT: B 201 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7914 (mmtt) REVERT: C 78 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7189 (tp30) REVERT: C 243 MET cc_start: 0.8811 (mmt) cc_final: 0.8582 (mmt) REVERT: C 258 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6742 (t80) outliers start: 21 outliers final: 6 residues processed: 108 average time/residue: 1.4371 time to fit residues: 162.6223 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7221 Z= 0.219 Angle : 0.601 6.450 9792 Z= 0.292 Chirality : 0.038 0.130 1101 Planarity : 0.004 0.038 1095 Dihedral : 16.756 114.290 1278 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.80 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 17.60 % Favored : 80.38 % 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: 2.93 (0.30), residues: 786 helix: 2.95 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.59 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS C 213 PHE 0.014 0.001 PHE C 272 TYR 0.012 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.676 Fit side-chains REVERT: A 14 LEU cc_start: 0.8712 (mt) cc_final: 0.8450 (mt) REVERT: A 247 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9059 (mt) REVERT: A 258 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.6580 (t80) REVERT: B 143 VAL cc_start: 0.8999 (t) cc_final: 0.8779 (t) REVERT: B 172 ARG cc_start: 0.6571 (tpm170) cc_final: 0.6144 (mmp80) REVERT: C 78 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7172 (tp30) REVERT: C 258 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6671 (t80) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 1.5043 time to fit residues: 159.0026 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7221 Z= 0.269 Angle : 0.633 6.844 9792 Z= 0.307 Chirality : 0.039 0.137 1101 Planarity : 0.004 0.038 1095 Dihedral : 16.971 117.405 1278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.56 % Rotamer: Outliers : 2.31 % Allowed : 17.32 % Favored : 80.38 % 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: 2.81 (0.29), residues: 786 helix: 2.85 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.58 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.002 PHE C 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.794 Fit side-chains REVERT: A 14 LEU cc_start: 0.8760 (mt) cc_final: 0.8473 (mt) REVERT: A 258 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.6706 (t80) REVERT: B 143 VAL cc_start: 0.9085 (t) cc_final: 0.8868 (t) REVERT: B 172 ARG cc_start: 0.6582 (tpm170) cc_final: 0.6158 (mmp80) REVERT: C 78 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7198 (tp30) REVERT: C 258 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6610 (t80) outliers start: 16 outliers final: 7 residues processed: 104 average time/residue: 1.5446 time to fit residues: 168.1301 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7221 Z= 0.244 Angle : 0.610 6.595 9792 Z= 0.295 Chirality : 0.038 0.133 1101 Planarity : 0.004 0.037 1095 Dihedral : 16.841 115.990 1278 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.31 % Favored : 96.31 % Rotamer: Outliers : 1.59 % Allowed : 17.75 % Favored : 80.66 % 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: 2.88 (0.29), residues: 786 helix: 2.90 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.57 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 76 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.002 PHE B 272 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.751 Fit side-chains REVERT: A 14 LEU cc_start: 0.8717 (mt) cc_final: 0.8439 (mt) REVERT: A 82 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7216 (mmm-85) REVERT: A 258 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.6634 (t80) REVERT: B 143 VAL cc_start: 0.9055 (t) cc_final: 0.8849 (t) REVERT: B 172 ARG cc_start: 0.6578 (tpm170) cc_final: 0.6270 (mmp80) REVERT: C 78 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7205 (tp30) REVERT: C 258 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6632 (t80) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 1.5930 time to fit residues: 166.3735 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094207 restraints weight = 8068.809| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.56 r_work: 0.2789 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7221 Z= 0.238 Angle : 0.618 7.811 9792 Z= 0.300 Chirality : 0.038 0.131 1101 Planarity : 0.004 0.038 1095 Dihedral : 16.747 111.103 1278 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.93 % Favored : 96.69 % Rotamer: Outliers : 2.16 % Allowed : 17.46 % Favored : 80.38 % 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: 2.87 (0.29), residues: 786 helix: 2.90 (0.19), residues: 627 sheet: None (None), residues: 0 loop : -2.58 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 76 HIS 0.002 0.001 HIS B 266 PHE 0.015 0.002 PHE C 272 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG C 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.51 seconds wall clock time: 54 minutes 47.51 seconds (3287.51 seconds total)