Starting phenix.real_space_refine on Thu Nov 14 11:59:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4b_45180/11_2024/9c4b_45180.cif" } resolution = 3.4 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= 0.042 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 1950 2.51 5 N 525 2.21 5 O 581 1.98 5 H 3030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6110 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 2 Time building chain proxies: 4.38, per 1000 atoms: 0.72 Number of scatterers: 6110 At special positions: 0 Unit cell: (81.9, 69.3, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 581 8.00 N 525 7.00 C 1950 6.00 H 3030 1.00 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=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 489.0 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 44.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.902A pdb=" N ALA A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.578A pdb=" N ILE A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.683A pdb=" N SER A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.536A pdb=" N CYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.642A pdb=" N LEU A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.627A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 422 through 428 removed outlier: 4.025A pdb=" N ARG A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.428A pdb=" N ILE A 18 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.574A pdb=" N VAL A 193 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 5.817A pdb=" N LEU A 168 " --> pdb=" O ILE A 349 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 357 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: 2.41 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3021 1.03 - 1.23: 13 1.23 - 1.42: 1310 1.42 - 1.62: 1797 1.62 - 1.81: 39 Bond restraints: 6180 Sorted by residual: bond pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N GLN A 281 " pdb=" CA GLN A 281 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.23e+01 bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.33e-02 5.65e+03 8.32e+00 bond pdb=" N GLU A 208 " pdb=" H GLU A 208 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 6175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11102 2.85 - 5.70: 52 5.70 - 8.56: 3 8.56 - 11.41: 1 11.41 - 14.26: 1 Bond angle restraints: 11159 Sorted by residual: angle pdb=" N GLN A 211 " pdb=" CA GLN A 211 " pdb=" C GLN A 211 " ideal model delta sigma weight residual 112.89 98.63 14.26 1.24e+00 6.50e-01 1.32e+02 angle pdb=" N ALA A 279 " pdb=" CA ALA A 279 " pdb=" C ALA A 279 " ideal model delta sigma weight residual 112.90 105.10 7.80 1.31e+00 5.83e-01 3.54e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 113.30 105.83 7.47 1.34e+00 5.57e-01 3.11e+01 angle pdb=" C PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta sigma weight residual 110.17 119.40 -9.23 1.69e+00 3.50e-01 2.98e+01 angle pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " pdb=" CG PHE A 210 " ideal model delta sigma weight residual 113.80 108.84 4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 11154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2546 17.69 - 35.39: 255 35.39 - 53.08: 89 53.08 - 70.77: 33 70.77 - 88.47: 9 Dihedral angle restraints: 2932 sinusoidal: 1599 harmonic: 1333 Sorted by residual: dihedral pdb=" C PHE A 210 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA LYS A 240 " pdb=" C LYS A 240 " pdb=" N GLU A 241 " pdb=" CA GLU A 241 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 223 " pdb=" C ILE A 223 " pdb=" N ALA A 224 " pdb=" CA ALA A 224 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 340 0.042 - 0.083: 86 0.083 - 0.125: 40 0.125 - 0.167: 4 0.167 - 0.209: 2 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA PHE A 210 " pdb=" N PHE A 210 " pdb=" C PHE A 210 " pdb=" CB PHE A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 92 " pdb=" N MET A 92 " pdb=" C MET A 92 " pdb=" CB MET A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA MET A 254 " pdb=" N MET A 254 " pdb=" C MET A 254 " pdb=" CB MET A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 469 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 211 " -0.254 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CD GLN A 211 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 211 " 0.241 2.00e-02 2.50e+03 pdb=" NE2 GLN A 211 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN A 211 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN A 211 " -0.510 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 281 " 0.141 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CD GLN A 281 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 281 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN A 281 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 281 " -0.226 2.00e-02 2.50e+03 pdb="HE22 GLN A 281 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 210 " 0.059 2.00e-02 2.50e+03 2.66e-02 2.12e+01 pdb=" CG PHE A 210 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 210 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 210 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 210 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 210 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 210 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 210 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 210 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 210 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 210 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 210 " 0.011 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 452 2.19 - 2.80: 12514 2.80 - 3.40: 17313 3.40 - 4.00: 22277 4.00 - 4.60: 33932 Nonbonded interactions: 86488 Sorted by model distance: nonbonded pdb=" O ALA A 74 " pdb="HH22 ARG A 79 " model vdw 1.593 2.450 nonbonded pdb=" O LEU A 168 " pdb=" H ILE A 349 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU A 46 " pdb=" H ARG A 47 " model vdw 1.652 2.450 nonbonded pdb=" H ALA A 125 " pdb=" OD1 ASN A 128 " model vdw 1.675 2.450 nonbonded pdb=" O GLY A 12 " pdb=" HD1 HIS A 118 " model vdw 1.706 2.450 ... (remaining 86483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.070 3150 Z= 0.249 Angle : 0.729 14.259 4272 Z= 0.462 Chirality : 0.047 0.209 472 Planarity : 0.004 0.044 554 Dihedral : 16.505 88.465 1163 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.94 % Favored : 93.28 % Rotamer: Outliers : 0.89 % Allowed : 20.71 % Favored : 78.40 % Cbeta Deviations : 0.27 % 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: -0.46 (0.44), residues: 387 helix: 0.72 (0.46), residues: 148 sheet: -0.65 (0.74), residues: 55 loop : -1.01 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.002 0.001 HIS A 105 PHE 0.045 0.002 PHE A 210 TYR 0.006 0.001 TYR A 253 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5729 (t80) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.3168 time to fit residues: 23.9164 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3150 Z= 0.201 Angle : 0.573 5.259 4272 Z= 0.309 Chirality : 0.044 0.154 472 Planarity : 0.005 0.044 554 Dihedral : 5.182 29.305 426 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.94 % Favored : 93.28 % Rotamer: Outliers : 1.78 % Allowed : 19.82 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.44), residues: 387 helix: 0.71 (0.43), residues: 156 sheet: -0.37 (0.78), residues: 55 loop : -0.99 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.005 0.001 HIS A 118 PHE 0.015 0.001 PHE A 210 TYR 0.016 0.001 TYR A 253 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.3303 time to fit residues: 25.1789 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 362 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7285 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3150 Z= 0.197 Angle : 0.551 5.303 4272 Z= 0.294 Chirality : 0.044 0.148 472 Planarity : 0.004 0.043 554 Dihedral : 5.067 28.242 424 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.72 % Favored : 92.76 % Rotamer: Outliers : 2.37 % Allowed : 19.82 % Favored : 77.81 % 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: -0.37 (0.45), residues: 387 helix: 0.67 (0.43), residues: 157 sheet: -0.37 (0.80), residues: 55 loop : -0.99 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 410 HIS 0.009 0.001 HIS A 105 PHE 0.012 0.001 PHE A 262 TYR 0.012 0.001 TYR A 253 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8378 (mttm) cc_final: 0.7964 (mmtp) REVERT: A 254 MET cc_start: 0.3382 (mmp) cc_final: 0.2976 (mmp) REVERT: A 263 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: A 289 PHE cc_start: 0.7086 (m-80) cc_final: 0.6846 (m-80) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.3682 time to fit residues: 29.2638 Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7321 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3150 Z= 0.263 Angle : 0.570 5.013 4272 Z= 0.306 Chirality : 0.043 0.148 472 Planarity : 0.005 0.046 554 Dihedral : 5.251 26.413 424 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.24 % Favored : 92.25 % Rotamer: Outliers : 3.25 % Allowed : 20.41 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.44), residues: 387 helix: 0.70 (0.44), residues: 155 sheet: -0.77 (0.73), residues: 60 loop : -1.24 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.007 0.001 HIS A 105 PHE 0.013 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5870 (mmp-170) cc_final: 0.5581 (mmp-170) REVERT: A 90 ASN cc_start: 0.8157 (t0) cc_final: 0.7954 (t0) REVERT: A 216 GLU cc_start: 0.7494 (tt0) cc_final: 0.6704 (mp0) REVERT: A 289 PHE cc_start: 0.7142 (m-80) cc_final: 0.6890 (m-80) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.3541 time to fit residues: 28.2077 Evaluate side-chains 71 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3150 Z= 0.201 Angle : 0.534 4.771 4272 Z= 0.283 Chirality : 0.043 0.144 472 Planarity : 0.005 0.045 554 Dihedral : 5.092 24.758 424 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.49 % Favored : 91.99 % Rotamer: Outliers : 2.96 % Allowed : 21.30 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.44), residues: 387 helix: 0.71 (0.44), residues: 155 sheet: -0.82 (0.72), residues: 60 loop : -1.16 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 96 HIS 0.007 0.001 HIS A 105 PHE 0.012 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5804 (mmp-170) cc_final: 0.5515 (mmp-170) REVERT: A 90 ASN cc_start: 0.8099 (t0) cc_final: 0.7850 (t0) REVERT: A 289 PHE cc_start: 0.7159 (m-80) cc_final: 0.6915 (m-80) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.4178 time to fit residues: 34.8226 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7290 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3150 Z= 0.172 Angle : 0.517 4.697 4272 Z= 0.271 Chirality : 0.042 0.139 472 Planarity : 0.004 0.044 554 Dihedral : 4.911 23.492 424 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.24 % Favored : 92.51 % Rotamer: Outliers : 3.25 % Allowed : 21.60 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.45), residues: 387 helix: 0.79 (0.44), residues: 157 sheet: -0.83 (0.72), residues: 60 loop : -1.19 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 410 HIS 0.006 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.0433 (OUTLIER) cc_final: 0.0108 (p) REVERT: A 47 ARG cc_start: 0.5730 (mmp-170) cc_final: 0.5417 (mmp-170) REVERT: A 90 ASN cc_start: 0.8086 (t0) cc_final: 0.7851 (t0) REVERT: A 248 ARG cc_start: 0.6754 (tpt170) cc_final: 0.6536 (tpm170) REVERT: A 289 PHE cc_start: 0.7125 (m-80) cc_final: 0.6860 (m-80) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.3493 time to fit residues: 29.9050 Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7302 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3150 Z= 0.203 Angle : 0.526 4.682 4272 Z= 0.278 Chirality : 0.043 0.140 472 Planarity : 0.005 0.044 554 Dihedral : 4.924 22.258 424 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 3.25 % Allowed : 20.71 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.45), residues: 387 helix: 0.84 (0.44), residues: 157 sheet: -0.93 (0.70), residues: 60 loop : -1.27 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.0563 (OUTLIER) cc_final: 0.0253 (p) REVERT: A 47 ARG cc_start: 0.5716 (mmp-170) cc_final: 0.5387 (mmp-170) REVERT: A 90 ASN cc_start: 0.8055 (t0) cc_final: 0.7827 (t0) REVERT: A 248 ARG cc_start: 0.6768 (tpt170) cc_final: 0.6553 (tpm170) REVERT: A 289 PHE cc_start: 0.7142 (m-80) cc_final: 0.6887 (m-80) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.3408 time to fit residues: 26.5343 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 27 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3150 Z= 0.156 Angle : 0.503 4.506 4272 Z= 0.263 Chirality : 0.043 0.136 472 Planarity : 0.004 0.044 554 Dihedral : 4.724 21.263 424 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.72 % Favored : 93.02 % Rotamer: Outliers : 1.78 % Allowed : 22.49 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.45), residues: 387 helix: 0.90 (0.44), residues: 157 sheet: -0.86 (0.70), residues: 60 loop : -1.16 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 410 HIS 0.005 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.006 0.001 TYR A 107 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5703 (mmp-170) cc_final: 0.5375 (mmp-170) REVERT: A 70 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7756 (mm) REVERT: A 90 ASN cc_start: 0.8023 (t0) cc_final: 0.7802 (t0) REVERT: A 248 ARG cc_start: 0.6732 (tpt170) cc_final: 0.6517 (tpm170) REVERT: A 289 PHE cc_start: 0.7104 (m-80) cc_final: 0.6850 (m-80) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.3440 time to fit residues: 25.6994 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7312 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3150 Z= 0.236 Angle : 0.537 4.660 4272 Z= 0.284 Chirality : 0.043 0.139 472 Planarity : 0.005 0.045 554 Dihedral : 4.870 21.361 424 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.72 % Favored : 93.02 % Rotamer: Outliers : 2.66 % Allowed : 21.01 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.45), residues: 387 helix: 0.88 (0.44), residues: 157 sheet: -1.12 (0.68), residues: 60 loop : -1.31 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.007 0.001 TYR A 186 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.0816 (OUTLIER) cc_final: 0.0529 (p) REVERT: A 47 ARG cc_start: 0.5784 (mmp-170) cc_final: 0.5474 (mmp-170) REVERT: A 70 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7789 (mm) REVERT: A 289 PHE cc_start: 0.7093 (m-80) cc_final: 0.6828 (m-80) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.3204 time to fit residues: 26.6467 Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.7276 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3150 Z= 0.164 Angle : 0.507 4.484 4272 Z= 0.267 Chirality : 0.042 0.137 472 Planarity : 0.004 0.044 554 Dihedral : 4.713 20.261 424 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.46 % Favored : 93.28 % Rotamer: Outliers : 1.78 % Allowed : 21.89 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.44), residues: 387 helix: 1.09 (0.45), residues: 149 sheet: -1.06 (0.68), residues: 60 loop : -1.20 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 410 HIS 0.004 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.006 0.001 TYR A 107 ARG 0.002 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5735 (mmp-170) cc_final: 0.5416 (mmp-170) REVERT: A 70 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 248 ARG cc_start: 0.6742 (tpt170) cc_final: 0.6529 (tpm170) REVERT: A 289 PHE cc_start: 0.7138 (m-80) cc_final: 0.6843 (m-80) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.3441 time to fit residues: 25.4144 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.152230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132735 restraints weight = 17957.649| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.77 r_work: 0.3721 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3150 Z= 0.176 Angle : 0.506 4.582 4272 Z= 0.265 Chirality : 0.042 0.136 472 Planarity : 0.004 0.045 554 Dihedral : 4.624 19.763 424 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 2.07 % Allowed : 21.60 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.45), residues: 387 helix: 1.11 (0.45), residues: 149 sheet: -1.40 (0.64), residues: 66 loop : -1.18 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.004 0.001 HIS A 105 PHE 0.010 0.001 PHE A 262 TYR 0.007 0.001 TYR A 68 ARG 0.001 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.02 seconds wall clock time: 57 minutes 56.77 seconds (3476.77 seconds total)