Starting phenix.real_space_refine on Sun Mar 10 19:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ght_40050/03_2024/8ght_40050_updated.pdb" } resolution = 3.05 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= 0.014 sd= 0.091 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 Cd 6 9.23 5 P 2 5.49 5 S 24 5.16 5 C 2818 2.51 5 N 740 2.21 5 O 776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2139 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "B" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2139 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Ad-hoc single atom residues: {' CD': 3} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Ad-hoc single atom residues: {' CD': 3} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CD CD B 503 " occ=0.60 Time building chain proxies: 2.88, per 1000 atoms: 0.66 Number of scatterers: 4366 At special positions: 0 Unit cell: (71.928, 83.916, 65.268, 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) Cd 6 47.96 S 24 16.00 P 2 15.00 O 776 8.00 N 740 7.00 C 2818 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=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 767.9 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.519A pdb=" N SER A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.870A pdb=" N ALA A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLY A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 119 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 123 through 145 Processing helix chain 'A' and resid 166 through 191 Proline residue: A 180 - end of helix removed outlier: 3.684A pdb=" N ALA A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 222 Proline residue: A 199 - end of helix Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 251 Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 255 through 277 Proline residue: A 259 - end of helix removed outlier: 4.748A pdb=" N ALA A 265 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 308 Processing helix chain 'B' and resid 7 through 21 removed outlier: 3.519A pdb=" N SER B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 53 through 80 removed outlier: 3.869A pdb=" N ALA B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLY B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 119 Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 123 through 145 Processing helix chain 'B' and resid 166 through 191 Proline residue: B 180 - end of helix removed outlier: 3.684A pdb=" N ALA B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 222 Proline residue: B 199 - end of helix Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 251 Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 255 through 277 Proline residue: B 259 - end of helix removed outlier: 4.747A pdb=" N ALA B 265 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 372 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 702 1.31 - 1.43: 1056 1.43 - 1.56: 2626 1.56 - 1.68: 4 1.68 - 1.81: 48 Bond restraints: 4436 Sorted by residual: bond pdb=" C8 PTY B 501 " pdb=" O7 PTY B 501 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C8 PTY A 404 " pdb=" O7 PTY A 404 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C30 PTY A 404 " pdb=" O4 PTY A 404 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C30 PTY B 501 " pdb=" O4 PTY B 501 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C6 PTY B 501 " pdb=" O7 PTY B 501 " ideal model delta sigma weight residual 1.432 1.398 0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 4431 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.20: 143 106.20 - 113.13: 2540 113.13 - 120.06: 1494 120.06 - 126.99: 1801 126.99 - 133.92: 56 Bond angle restraints: 6034 Sorted by residual: angle pdb=" O11 PTY A 404 " pdb=" P1 PTY A 404 " pdb=" O14 PTY A 404 " ideal model delta sigma weight residual 92.90 109.42 -16.52 3.00e+00 1.11e-01 3.03e+01 angle pdb=" O11 PTY B 501 " pdb=" P1 PTY B 501 " pdb=" O14 PTY B 501 " ideal model delta sigma weight residual 92.90 109.40 -16.50 3.00e+00 1.11e-01 3.02e+01 angle pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" C THR A 281 " ideal model delta sigma weight residual 114.56 110.19 4.37 1.27e+00 6.20e-01 1.19e+01 angle pdb=" N THR B 281 " pdb=" CA THR B 281 " pdb=" C THR B 281 " ideal model delta sigma weight residual 114.56 110.19 4.37 1.27e+00 6.20e-01 1.18e+01 angle pdb=" O12 PTY A 404 " pdb=" P1 PTY A 404 " pdb=" O13 PTY A 404 " ideal model delta sigma weight residual 119.61 110.02 9.59 3.00e+00 1.11e-01 1.02e+01 ... (remaining 6029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.09: 2522 33.09 - 66.18: 62 66.18 - 99.27: 6 99.27 - 132.36: 0 132.36 - 165.45: 2 Dihedral angle restraints: 2592 sinusoidal: 928 harmonic: 1664 Sorted by residual: dihedral pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" N PRO A 279 " pdb=" CA PRO A 279 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ILE B 278 " pdb=" C ILE B 278 " pdb=" N PRO B 279 " pdb=" CA PRO B 279 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C3 PTY B 501 " pdb=" O11 PTY B 501 " pdb=" P1 PTY B 501 " pdb=" O12 PTY B 501 " ideal model delta sinusoidal sigma weight residual 300.23 134.78 165.45 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 2589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 412 0.023 - 0.047: 185 0.047 - 0.070: 80 0.070 - 0.094: 39 0.094 - 0.117: 22 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO A 180 " pdb=" N PRO A 180 " pdb=" C PRO A 180 " pdb=" CB PRO A 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA ASN A 178 " pdb=" N ASN A 178 " pdb=" C ASN A 178 " pdb=" CB ASN A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.20e-01 ... (remaining 735 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 274 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C SER B 274 " -0.055 2.00e-02 2.50e+03 pdb=" O SER B 274 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS B 275 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 274 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C SER A 274 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 274 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 275 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL B 272 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL B 273 " -0.018 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1098 2.80 - 3.32: 4619 3.32 - 3.85: 7319 3.85 - 4.37: 7926 4.37 - 4.90: 14059 Nonbonded interactions: 35021 Sorted by model distance: nonbonded pdb=" OD2 ASP B 208 " pdb=" OE2 GLU B 240 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP A 208 " pdb=" OE2 GLU A 240 " model vdw 2.272 3.040 nonbonded pdb=" CE1 HIS B 151 " pdb=" OE1 GLU B 276 " model vdw 2.282 3.260 nonbonded pdb=" CE1 HIS A 151 " pdb=" OE1 GLU A 276 " model vdw 2.282 3.260 nonbonded pdb=" OD1 ASP A 144 " pdb=" CE1 HIS A 149 " model vdw 2.285 3.260 ... (remaining 35016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 309 or resid 402 through 403)) selection = (chain 'B' and (resid 6 through 309 or resid 502 through 503)) } 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=0.60 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: 0.230 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: 0.710 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4436 Z= 0.304 Angle : 0.871 16.520 6034 Z= 0.418 Chirality : 0.038 0.117 738 Planarity : 0.006 0.041 764 Dihedral : 15.440 165.450 1540 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.62 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 1.91 (0.35), residues: 604 helix: 2.27 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -3.12 (0.47), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 168 HIS 0.006 0.001 HIS B 149 PHE 0.010 0.002 PHE A 94 TYR 0.016 0.002 TYR B 145 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 89 ASP cc_start: 0.8787 (m-30) cc_final: 0.8524 (m-30) REVERT: B 157 GLN cc_start: 0.7995 (mm110) cc_final: 0.7716 (tt0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1586 time to fit residues: 21.7472 Evaluate side-chains 76 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4436 Z= 0.191 Angle : 0.620 6.839 6034 Z= 0.307 Chirality : 0.036 0.114 738 Planarity : 0.005 0.039 764 Dihedral : 10.218 109.918 702 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.12 % Favored : 92.55 % Rotamer: Outliers : 1.94 % Allowed : 12.38 % Favored : 85.68 % 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: 2.22 (0.37), residues: 604 helix: 2.52 (0.25), residues: 482 sheet: None (None), residues: 0 loop : -3.21 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 168 HIS 0.006 0.001 HIS A 55 PHE 0.010 0.001 PHE B 189 TYR 0.009 0.001 TYR B 145 ARG 0.010 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.459 Fit side-chains REVERT: A 145 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 193 ASP cc_start: 0.7789 (t0) cc_final: 0.7466 (t0) REVERT: B 75 LEU cc_start: 0.9485 (mm) cc_final: 0.9217 (mm) REVERT: B 89 ASP cc_start: 0.8746 (m-30) cc_final: 0.8455 (m-30) REVERT: B 295 MET cc_start: 0.9232 (mmm) cc_final: 0.8943 (mmm) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.1074 time to fit residues: 14.3250 Evaluate side-chains 79 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 298 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4436 Z= 0.401 Angle : 0.736 8.942 6034 Z= 0.367 Chirality : 0.040 0.129 738 Planarity : 0.005 0.037 764 Dihedral : 8.924 60.568 702 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.45 % Favored : 92.22 % Rotamer: Outliers : 3.64 % Allowed : 16.02 % Favored : 80.34 % 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: 2.05 (0.36), residues: 604 helix: 2.43 (0.24), residues: 478 sheet: None (None), residues: 0 loop : -3.22 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.005 0.001 HIS A 55 PHE 0.014 0.002 PHE A 94 TYR 0.010 0.001 TYR B 145 ARG 0.002 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.441 Fit side-chains REVERT: A 98 MET cc_start: 0.9245 (tpp) cc_final: 0.8947 (tpp) REVERT: A 238 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 280 GLU cc_start: 0.7720 (mp0) cc_final: 0.7345 (mp0) REVERT: A 303 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8451 (t80) REVERT: B 89 ASP cc_start: 0.8891 (m-30) cc_final: 0.8508 (m-30) REVERT: B 262 MET cc_start: 0.9127 (mmm) cc_final: 0.8633 (tpp) outliers start: 15 outliers final: 6 residues processed: 81 average time/residue: 0.1113 time to fit residues: 12.4632 Evaluate side-chains 74 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4436 Z= 0.212 Angle : 0.617 7.029 6034 Z= 0.307 Chirality : 0.037 0.119 738 Planarity : 0.005 0.040 764 Dihedral : 7.997 59.983 702 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.79 % Favored : 92.88 % Rotamer: Outliers : 3.16 % Allowed : 17.72 % Favored : 79.13 % 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: 2.31 (0.37), residues: 604 helix: 2.54 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.17 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 168 HIS 0.005 0.001 HIS A 55 PHE 0.012 0.001 PHE A 94 TYR 0.007 0.001 TYR B 145 ARG 0.003 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.469 Fit side-chains REVERT: A 98 MET cc_start: 0.9172 (tpp) cc_final: 0.8935 (tpp) REVERT: A 262 MET cc_start: 0.9053 (mmm) cc_final: 0.8476 (tpp) REVERT: A 280 GLU cc_start: 0.7666 (mp0) cc_final: 0.7376 (mp0) REVERT: A 303 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8694 (t80) REVERT: B 89 ASP cc_start: 0.8874 (m-30) cc_final: 0.8444 (m-30) REVERT: B 157 GLN cc_start: 0.8071 (mm110) cc_final: 0.7854 (mm110) REVERT: B 262 MET cc_start: 0.9042 (mmm) cc_final: 0.8415 (mmm) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.1164 time to fit residues: 13.6072 Evaluate side-chains 81 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4436 Z= 0.189 Angle : 0.601 7.047 6034 Z= 0.296 Chirality : 0.036 0.112 738 Planarity : 0.005 0.040 764 Dihedral : 7.250 57.773 702 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.12 % Favored : 92.55 % Rotamer: Outliers : 3.16 % Allowed : 18.20 % Favored : 78.64 % 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: 2.40 (0.37), residues: 604 helix: 2.72 (0.24), residues: 478 sheet: None (None), residues: 0 loop : -3.31 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 168 HIS 0.005 0.001 HIS A 55 PHE 0.010 0.001 PHE A 94 TYR 0.005 0.001 TYR B 145 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.464 Fit side-chains REVERT: A 98 MET cc_start: 0.9136 (tpp) cc_final: 0.8833 (mmt) REVERT: A 262 MET cc_start: 0.8956 (mmm) cc_final: 0.8433 (tpp) REVERT: A 280 GLU cc_start: 0.7591 (mp0) cc_final: 0.7322 (mp0) REVERT: B 67 PHE cc_start: 0.9125 (t80) cc_final: 0.8745 (t80) REVERT: B 89 ASP cc_start: 0.8789 (m-30) cc_final: 0.8409 (m-30) REVERT: B 262 MET cc_start: 0.8971 (mmm) cc_final: 0.8390 (tpp) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.1116 time to fit residues: 13.6541 Evaluate side-chains 84 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4436 Z= 0.194 Angle : 0.595 5.697 6034 Z= 0.298 Chirality : 0.036 0.116 738 Planarity : 0.005 0.040 764 Dihedral : 6.959 56.023 702 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.45 % Favored : 92.22 % Rotamer: Outliers : 3.64 % Allowed : 20.39 % Favored : 75.97 % 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: 2.37 (0.36), residues: 604 helix: 2.72 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -3.26 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 168 HIS 0.005 0.001 HIS A 55 PHE 0.009 0.001 PHE A 94 TYR 0.004 0.000 TYR B 145 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.485 Fit side-chains REVERT: A 67 PHE cc_start: 0.9235 (t80) cc_final: 0.8967 (t80) REVERT: A 207 GLN cc_start: 0.8568 (pp30) cc_final: 0.7732 (pp30) REVERT: A 262 MET cc_start: 0.8939 (mmm) cc_final: 0.8422 (tpp) REVERT: A 280 GLU cc_start: 0.7540 (mp0) cc_final: 0.7100 (mp0) REVERT: A 298 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9029 (t80) REVERT: B 67 PHE cc_start: 0.9157 (t80) cc_final: 0.8665 (t80) REVERT: B 89 ASP cc_start: 0.8773 (m-30) cc_final: 0.8403 (m-30) REVERT: B 207 GLN cc_start: 0.7954 (pp30) cc_final: 0.7702 (pp30) REVERT: B 262 MET cc_start: 0.8983 (mmm) cc_final: 0.8393 (mmm) REVERT: B 280 GLU cc_start: 0.7746 (mp0) cc_final: 0.7297 (mp0) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1151 time to fit residues: 14.4889 Evaluate side-chains 92 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- 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: 0.8197 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4436 Z= 0.219 Angle : 0.606 5.728 6034 Z= 0.306 Chirality : 0.037 0.122 738 Planarity : 0.005 0.039 764 Dihedral : 6.871 54.482 702 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.12 % Favored : 92.55 % Rotamer: Outliers : 4.37 % Allowed : 20.39 % Favored : 75.24 % 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: 2.37 (0.36), residues: 604 helix: 2.64 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -3.11 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 168 HIS 0.005 0.001 HIS A 55 PHE 0.010 0.001 PHE A 94 TYR 0.004 0.000 TYR B 145 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.486 Fit side-chains REVERT: A 262 MET cc_start: 0.8989 (mmm) cc_final: 0.8485 (tpp) REVERT: A 280 GLU cc_start: 0.7552 (mp0) cc_final: 0.7188 (mp0) REVERT: A 298 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9026 (t80) REVERT: B 67 PHE cc_start: 0.9220 (t80) cc_final: 0.8661 (t80) REVERT: B 89 ASP cc_start: 0.8792 (m-30) cc_final: 0.8413 (m-30) REVERT: B 207 GLN cc_start: 0.8076 (pp30) cc_final: 0.7834 (pp30) REVERT: B 262 MET cc_start: 0.9001 (mmm) cc_final: 0.8351 (mmm) REVERT: B 280 GLU cc_start: 0.7648 (mp0) cc_final: 0.7149 (mp0) outliers start: 18 outliers final: 11 residues processed: 90 average time/residue: 0.1129 time to fit residues: 14.1349 Evaluate side-chains 89 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4436 Z= 0.265 Angle : 0.643 6.222 6034 Z= 0.325 Chirality : 0.037 0.116 738 Planarity : 0.005 0.038 764 Dihedral : 7.006 53.591 702 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.62 % Favored : 92.05 % Rotamer: Outliers : 3.40 % Allowed : 21.60 % 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: 2.32 (0.37), residues: 604 helix: 2.64 (0.25), residues: 478 sheet: None (None), residues: 0 loop : -3.20 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 168 HIS 0.006 0.001 HIS A 55 PHE 0.011 0.001 PHE A 94 TYR 0.004 0.001 TYR B 145 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.496 Fit side-chains REVERT: A 262 MET cc_start: 0.9023 (mmm) cc_final: 0.8482 (tpp) REVERT: A 278 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (mm) REVERT: A 298 PHE cc_start: 0.9487 (OUTLIER) cc_final: 0.9119 (t80) REVERT: B 89 ASP cc_start: 0.8833 (m-30) cc_final: 0.8454 (m-30) REVERT: B 262 MET cc_start: 0.9054 (mmm) cc_final: 0.8311 (mmm) REVERT: B 280 GLU cc_start: 0.7653 (mp0) cc_final: 0.7109 (mp0) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1127 time to fit residues: 13.0369 Evaluate side-chains 87 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 284 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4436 Z= 0.194 Angle : 0.628 8.087 6034 Z= 0.316 Chirality : 0.036 0.138 738 Planarity : 0.005 0.040 764 Dihedral : 6.513 52.329 702 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 3.40 % Allowed : 22.82 % Favored : 73.79 % 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: 2.26 (0.37), residues: 604 helix: 2.49 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.20 (0.47), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 168 HIS 0.005 0.001 HIS A 282 PHE 0.011 0.001 PHE A 94 TYR 0.005 0.001 TYR B 145 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.436 Fit side-chains REVERT: A 67 PHE cc_start: 0.9233 (t80) cc_final: 0.8939 (t80) REVERT: A 262 MET cc_start: 0.8890 (mmm) cc_final: 0.8375 (tpp) REVERT: A 298 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8903 (t80) REVERT: B 67 PHE cc_start: 0.9192 (t80) cc_final: 0.8910 (t80) REVERT: B 89 ASP cc_start: 0.8692 (m-30) cc_final: 0.8345 (m-30) REVERT: B 262 MET cc_start: 0.8949 (mmm) cc_final: 0.8277 (tpp) REVERT: B 280 GLU cc_start: 0.7684 (mp0) cc_final: 0.7157 (mp0) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1344 time to fit residues: 17.2158 Evaluate side-chains 93 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.0000 chunk 19 optimal weight: 0.9980 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4436 Z= 0.202 Angle : 0.644 8.159 6034 Z= 0.321 Chirality : 0.036 0.131 738 Planarity : 0.005 0.039 764 Dihedral : 6.295 50.138 702 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.12 % Favored : 92.55 % Rotamer: Outliers : 3.16 % Allowed : 23.30 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.36), residues: 604 helix: 2.53 (0.24), residues: 486 sheet: None (None), residues: 0 loop : -3.53 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 168 HIS 0.004 0.001 HIS A 55 PHE 0.012 0.001 PHE A 94 TYR 0.004 0.000 TYR B 145 ARG 0.002 0.000 ARG A 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.490 Fit side-chains REVERT: A 67 PHE cc_start: 0.9238 (t80) cc_final: 0.8929 (t80) REVERT: A 262 MET cc_start: 0.8905 (mmm) cc_final: 0.8360 (tpp) REVERT: A 280 GLU cc_start: 0.7543 (mp0) cc_final: 0.7239 (mp0) REVERT: A 295 MET cc_start: 0.9298 (mmm) cc_final: 0.8943 (mmm) REVERT: A 298 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8974 (t80) REVERT: B 67 PHE cc_start: 0.9209 (t80) cc_final: 0.8913 (t80) REVERT: B 89 ASP cc_start: 0.8741 (m-30) cc_final: 0.8365 (m-30) REVERT: B 262 MET cc_start: 0.8983 (mmm) cc_final: 0.8339 (mmm) REVERT: B 280 GLU cc_start: 0.7646 (mp0) cc_final: 0.7173 (mp0) outliers start: 13 outliers final: 12 residues processed: 89 average time/residue: 0.1200 time to fit residues: 14.4996 Evaluate side-chains 91 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.089917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072584 restraints weight = 5482.003| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.05 r_work: 0.2959 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4436 Z= 0.211 Angle : 0.640 7.158 6034 Z= 0.321 Chirality : 0.036 0.128 738 Planarity : 0.005 0.038 764 Dihedral : 6.160 47.417 702 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.95 % Favored : 92.72 % Rotamer: Outliers : 3.16 % Allowed : 23.79 % Favored : 73.06 % 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: 2.19 (0.36), residues: 604 helix: 2.51 (0.24), residues: 486 sheet: None (None), residues: 0 loop : -3.49 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 168 HIS 0.004 0.001 HIS A 55 PHE 0.012 0.001 PHE A 94 TYR 0.004 0.000 TYR B 145 ARG 0.001 0.000 ARG A 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.27 seconds wall clock time: 20 minutes 55.63 seconds (1255.63 seconds total)