Starting phenix.real_space_refine on Fri Dec 27 07:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176.map" model { file = "/net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goe_34176/12_2024/8goe_34176_neut.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2204 2.51 5 N 555 2.21 5 O 554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3323 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3290 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 bond proxies already assigned to first conformer: 3334 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1, 33 Unusual residues: {'THH': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 133 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 133 " occ=0.50 residue: pdb=" N AARG A 208 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 208 " occ=0.50 Time building chain proxies: 4.60, per 1000 atoms: 1.38 Number of scatterers: 3323 At special positions: 0 Unit cell: (78, 73, 67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 554 8.00 N 555 7.00 C 2204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 714.4 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB THH A 601 " Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 25 through 39 removed outlier: 3.754A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.778A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.662A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 113 removed outlier: 3.559A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 4.280A pdb=" N SER A 137 " --> pdb=" O AARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.611A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 176 removed outlier: 4.722A pdb=" N GLN A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.741A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.772A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.741A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.552A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.534A pdb=" N ARG A 303 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 325 removed outlier: 3.624A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.517A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 427 through 453 removed outlier: 3.607A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.89 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: 472 1.31 - 1.43: 1057 1.43 - 1.56: 1871 1.56 - 1.68: 1 1.68 - 1.81: 16 Bond restraints: 3417 Sorted by residual: bond pdb=" C4 THH A 601 " pdb=" O4 THH A 601 " ideal model delta sigma weight residual 1.347 1.184 0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N8 THH A 601 " pdb=" C8AATHH A 601 " ideal model delta sigma weight residual 1.351 1.508 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" N THH A 601 " pdb=" C THH A 601 " ideal model delta sigma weight residual 1.346 1.479 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" N5 THH A 601 " pdb=" C4AATHH A 601 " ideal model delta sigma weight residual 1.419 1.504 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C15 THH A 601 " pdb=" N10 THH A 601 " ideal model delta sigma weight residual 1.379 1.460 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 3412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4505 1.96 - 3.91: 117 3.91 - 5.87: 24 5.87 - 7.83: 12 7.83 - 9.79: 1 Bond angle restraints: 4659 Sorted by residual: angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 111.23 101.44 9.79 1.63e+00 3.76e-01 3.60e+01 angle pdb=" N GLN A 120 " pdb=" CA GLN A 120 " pdb=" C GLN A 120 " ideal model delta sigma weight residual 111.36 105.80 5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" CA VAL A 327 " pdb=" CB VAL A 327 " pdb=" CG1 VAL A 327 " ideal model delta sigma weight residual 110.40 115.30 -4.90 1.70e+00 3.46e-01 8.30e+00 angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 115.98 -6.17 2.21e+00 2.05e-01 7.79e+00 angle pdb=" CA THR A 49 " pdb=" C THR A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 118.44 122.66 -4.22 1.59e+00 3.96e-01 7.06e+00 ... (remaining 4654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 1687 11.92 - 23.84: 206 23.84 - 35.75: 57 35.75 - 47.67: 15 47.67 - 59.59: 18 Dihedral angle restraints: 1983 sinusoidal: 777 harmonic: 1206 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU A 452 " pdb=" C LEU A 452 " pdb=" N ASP A 453 " pdb=" CA ASP A 453 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A 253 " pdb=" CD ARG A 253 " pdb=" NE ARG A 253 " pdb=" CZ ARG A 253 " ideal model delta sinusoidal sigma weight residual 90.00 133.63 -43.63 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 345 0.039 - 0.077: 151 0.077 - 0.116: 29 0.116 - 0.155: 8 0.155 - 0.193: 4 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA LEU A 121 " pdb=" N LEU A 121 " pdb=" C LEU A 121 " pdb=" CB LEU A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 534 not shown) Planarity restraints: 565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 70 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE A 41 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 82 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.030 5.00e-02 4.00e+02 ... (remaining 562 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 997 2.80 - 3.32: 2989 3.32 - 3.85: 5671 3.85 - 4.37: 7086 4.37 - 4.90: 11737 Nonbonded interactions: 28480 Sorted by model distance: nonbonded pdb=" NH2 ARG A 42 " pdb=" OE2 GLU A 45 " model vdw 2.273 3.120 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 64 " pdb=" OG1 THR A 69 " model vdw 2.296 3.040 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 126 " model vdw 2.313 3.040 ... (remaining 28475 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=0.50 max=1.00 mean=0.99 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: 1.350 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.060 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.008 0.163 3417 Z= 0.511 Angle : 0.851 9.785 4659 Z= 0.468 Chirality : 0.046 0.193 537 Planarity : 0.006 0.061 565 Dihedral : 13.131 59.587 1209 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.57 % Allowed : 8.50 % Favored : 90.93 % Cbeta Deviations : 0.26 % 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: -6.19 (0.23), residues: 409 helix: -4.26 (0.12), residues: 323 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.002 PHE A 37 TYR 0.008 0.001 TYR A 92 ARG 0.004 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.380 Fit side-chains REVERT: A 88 ASP cc_start: 0.8379 (t70) cc_final: 0.8063 (t70) REVERT: A 294 GLU cc_start: 0.8068 (tt0) cc_final: 0.7688 (tt0) REVERT: A 445 ILE cc_start: 0.8561 (mt) cc_final: 0.8268 (mt) REVERT: A 452 LEU cc_start: 0.7280 (mt) cc_final: 0.7038 (mt) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 1.0941 time to fit residues: 61.0817 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 266 GLN A 277 ASN A 377 GLN A 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.201 Angle : 0.566 9.087 4659 Z= 0.293 Chirality : 0.038 0.105 537 Planarity : 0.005 0.036 565 Dihedral : 7.466 57.705 493 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.57 % Allowed : 10.20 % Favored : 89.24 % Cbeta Deviations : 0.26 % 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: -2.63 (0.34), residues: 409 helix: -1.53 (0.24), residues: 322 sheet: None (None), residues: 0 loop : -1.74 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.015 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.6969 (mm) REVERT: A 294 GLU cc_start: 0.7895 (tt0) cc_final: 0.7475 (tt0) REVERT: A 452 LEU cc_start: 0.7055 (mt) cc_final: 0.6828 (mt) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.8853 time to fit residues: 37.1766 Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3417 Z= 0.175 Angle : 0.513 7.873 4659 Z= 0.259 Chirality : 0.037 0.109 537 Planarity : 0.004 0.029 565 Dihedral : 6.592 49.374 492 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % Favored : 88.39 % Cbeta Deviations : 0.26 % 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: -0.44 (0.39), residues: 409 helix: 0.11 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -1.31 (0.54), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.024 0.001 PHE A 322 TYR 0.008 0.001 TYR A 149 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7179 (mtt180) cc_final: 0.6782 (mmm160) REVERT: A 161 LEU cc_start: 0.7561 (pp) cc_final: 0.7120 (mm) REVERT: A 294 GLU cc_start: 0.7952 (tt0) cc_final: 0.7498 (tt0) REVERT: A 452 LEU cc_start: 0.7017 (mt) cc_final: 0.6805 (mt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 1.0917 time to fit residues: 50.0390 Evaluate side-chains 40 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 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 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.216 Angle : 0.529 8.913 4659 Z= 0.264 Chirality : 0.039 0.118 537 Planarity : 0.003 0.025 565 Dihedral : 6.303 43.956 492 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.57 % Allowed : 13.03 % Favored : 86.40 % Cbeta Deviations : 0.26 % 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: 0.22 (0.40), residues: 409 helix: 0.54 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.01 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 372 TYR 0.011 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7535 (pp) cc_final: 0.7307 (mp) REVERT: A 294 GLU cc_start: 0.8135 (tt0) cc_final: 0.7829 (tt0) REVERT: A 452 LEU cc_start: 0.6992 (mt) cc_final: 0.6778 (mt) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.9786 time to fit residues: 36.9323 Evaluate side-chains 35 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3417 Z= 0.251 Angle : 0.541 9.045 4659 Z= 0.269 Chirality : 0.040 0.119 537 Planarity : 0.003 0.025 565 Dihedral : 6.251 42.285 492 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.13 % Allowed : 11.90 % Favored : 86.97 % Cbeta Deviations : 0.26 % 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: 0.49 (0.41), residues: 409 helix: 0.71 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.001 PHE A 322 TYR 0.011 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 256 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.7034 (ttp80) REVERT: A 294 GLU cc_start: 0.8181 (tt0) cc_final: 0.7850 (tt0) REVERT: A 452 LEU cc_start: 0.7029 (mt) cc_final: 0.6822 (mt) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.9180 time to fit residues: 35.6482 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7838 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3417 Z= 0.246 Angle : 0.536 9.043 4659 Z= 0.267 Chirality : 0.040 0.117 537 Planarity : 0.003 0.025 565 Dihedral : 6.091 40.035 492 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.70 % Allowed : 11.05 % Favored : 87.25 % Cbeta Deviations : 0.26 % 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: 0.74 (0.41), residues: 409 helix: 0.89 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.77 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 294 GLU cc_start: 0.8160 (tt0) cc_final: 0.7851 (tt0) REVERT: A 452 LEU cc_start: 0.7077 (mt) cc_final: 0.6868 (mt) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 1.0542 time to fit residues: 42.7562 Evaluate side-chains 38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3417 Z= 0.237 Angle : 0.539 9.161 4659 Z= 0.267 Chirality : 0.039 0.115 537 Planarity : 0.003 0.029 565 Dihedral : 5.970 38.528 492 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 12.18 % Favored : 86.97 % Cbeta Deviations : 0.26 % 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: 0.91 (0.41), residues: 409 helix: 1.02 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.75 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.001 PHE A 322 TYR 0.011 0.001 TYR A 155 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7116 (mm) REVERT: A 294 GLU cc_start: 0.8163 (tt0) cc_final: 0.7853 (tt0) REVERT: A 330 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7453 (mtm-85) REVERT: A 452 LEU cc_start: 0.7092 (mt) cc_final: 0.6887 (mt) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.0534 time to fit residues: 42.7230 Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.219 Angle : 0.528 9.280 4659 Z= 0.262 Chirality : 0.039 0.113 537 Planarity : 0.003 0.028 565 Dihedral : 5.791 36.512 492 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 11.90 % Favored : 87.25 % Cbeta Deviations : 0.26 % 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: 1.11 (0.41), residues: 409 helix: 1.17 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.71 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.007 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7136 (mm) REVERT: A 294 GLU cc_start: 0.8083 (tt0) cc_final: 0.7789 (tt0) REVERT: A 330 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7345 (mtm-85) REVERT: A 452 LEU cc_start: 0.7079 (mt) cc_final: 0.6878 (mt) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.9859 time to fit residues: 39.1675 Evaluate side-chains 38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.205 Angle : 0.523 9.353 4659 Z= 0.258 Chirality : 0.039 0.111 537 Planarity : 0.003 0.025 565 Dihedral : 5.605 34.207 492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 12.75 % Favored : 86.69 % Cbeta Deviations : 0.26 % 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: 1.29 (0.42), residues: 409 helix: 1.30 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.68 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.027 0.001 PHE A 322 TYR 0.011 0.001 TYR A 155 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7140 (mm) REVERT: A 294 GLU cc_start: 0.8084 (tt0) cc_final: 0.7788 (tt0) REVERT: A 452 LEU cc_start: 0.7084 (mt) cc_final: 0.6880 (mt) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.9474 time to fit residues: 34.7624 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3417 Z= 0.154 Angle : 0.497 9.419 4659 Z= 0.247 Chirality : 0.037 0.114 537 Planarity : 0.003 0.025 565 Dihedral : 5.324 31.297 492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.57 % Allowed : 12.46 % Favored : 86.97 % Cbeta Deviations : 0.26 % 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: 1.53 (0.42), residues: 409 helix: 1.49 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -0.65 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.014 0.001 PHE A 372 TYR 0.008 0.001 TYR A 149 ARG 0.004 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7102 (mm) REVERT: A 294 GLU cc_start: 0.8078 (tt0) cc_final: 0.7786 (tt0) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 1.0125 time to fit residues: 38.1139 Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.098487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.078194 restraints weight = 15899.952| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.27 r_work: 0.2655 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.201 Angle : 0.527 9.384 4659 Z= 0.259 Chirality : 0.039 0.111 537 Planarity : 0.003 0.027 565 Dihedral : 5.359 30.874 492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 12.75 % Favored : 86.40 % Cbeta Deviations : 0.26 % 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: 1.55 (0.42), residues: 409 helix: 1.51 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.63 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.029 0.001 PHE A 322 TYR 0.013 0.001 TYR A 155 ARG 0.008 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.52 seconds wall clock time: 28 minutes 11.76 seconds (1691.76 seconds total)