Starting phenix.real_space_refine on Mon Sep 23 15:15:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/09_2024/7lcj_23275.cif" } resolution = 2.82 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 571 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3264 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 58 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 17} Link IDs: {None: 17} Time building chain proxies: 3.00, per 1000 atoms: 0.92 Number of scatterers: 3264 At special positions: 0 Unit cell: (60.079, 116.866, 69.955, 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 18 16.00 F 1 9.00 O 571 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 336.3 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 70.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.918A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.604A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 Processing helix chain 'R' and resid 202 through 207 removed outlier: 3.510A pdb=" N SER R 206 " --> pdb=" O LYS R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 3.944A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.705A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.800A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.848A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing helix chain 'R' and resid 377 through 392 Processing helix chain 'R' and resid 393 through 404 Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.547A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 597 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: 0.82 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 974 1.41 - 1.54: 1861 1.54 - 1.68: 6 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.44e-02 4.82e+03 1.17e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 4503 3.63 - 7.26: 63 7.26 - 10.88: 3 10.88 - 14.51: 1 14.51 - 18.14: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" C SER R 136 " pdb=" N PRO R 137 " pdb=" CA PRO R 137 " ideal model delta sigma weight residual 119.28 126.40 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta sigma weight residual 110.67 122.36 -11.69 1.92e+00 2.71e-01 3.71e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.12 18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C LEU R 89 " pdb=" N PRO R 90 " pdb=" CA PRO R 90 " ideal model delta sigma weight residual 119.28 125.52 -6.24 1.10e+00 8.26e-01 3.21e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.79 119.63 -8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1743 17.85 - 35.70: 157 35.70 - 53.55: 27 53.55 - 71.39: 3 71.39 - 89.24: 2 Dihedral angle restraints: 1932 sinusoidal: 776 harmonic: 1156 Sorted by residual: dihedral pdb=" C THR R 362 " pdb=" N THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta harmonic sigma weight residual -122.00 -143.04 21.04 0 2.50e+00 1.60e-01 7.08e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -142.72 56.72 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 466 0.145 - 0.290: 27 0.290 - 0.435: 2 0.435 - 0.580: 1 0.580 - 0.724: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR R 362 " pdb=" N THR R 362 " pdb=" C THR R 362 " pdb=" CB THR R 362 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA TRP R 243 " pdb=" N TRP R 243 " pdb=" C TRP R 243 " pdb=" CB TRP R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 355 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR R 355 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 355 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 356 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ILE R 146 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 277 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " 0.027 5.00e-02 4.00e+02 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 3196 3.29 - 3.83: 5221 3.83 - 4.36: 6319 4.36 - 4.90: 10614 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.216 3.120 nonbonded pdb=" O GLY R 98 " pdb=" ND1 HIS R 99 " model vdw 2.335 3.120 nonbonded pdb=" O GLU R 408 " pdb=" OE1 GLU R 412 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU R 76 " pdb=" OG SER R 79 " model vdw 2.342 3.040 nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.383 3.120 ... (remaining 25782 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=0.00 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: 1.420 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: 0.030 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.011 0.114 3351 Z= 0.669 Angle : 1.188 18.141 4571 Z= 0.785 Chirality : 0.083 0.724 497 Planarity : 0.006 0.049 557 Dihedral : 13.407 89.243 1172 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.67 % Cbeta Deviations : 0.80 % 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: 0.54 (0.41), residues: 386 helix: 1.08 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.006 0.002 HIS R 180 PHE 0.017 0.003 PHE R 280 TYR 0.023 0.003 TYR R 148 ARG 0.003 0.001 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.619 Fit side-chains REVERT: R 41 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6643 (mm-30) REVERT: R 416 SER cc_start: 0.6812 (t) cc_final: 0.6581 (m) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.9855 time to fit residues: 37.0757 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.189 Angle : 0.589 7.195 4571 Z= 0.314 Chirality : 0.038 0.145 497 Planarity : 0.004 0.051 557 Dihedral : 5.304 30.069 458 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.45 % Allowed : 8.43 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.42), residues: 386 helix: 1.94 (0.32), residues: 255 sheet: None (None), residues: 0 loop : -0.82 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 PHE 0.014 0.002 PHE R 143 TYR 0.028 0.002 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.335 Fit side-chains REVERT: R 41 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6638 (mm-30) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.7555 time to fit residues: 26.3369 Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 35 optimal weight: 0.0980 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3351 Z= 0.244 Angle : 0.587 10.914 4571 Z= 0.305 Chirality : 0.039 0.141 497 Planarity : 0.004 0.058 557 Dihedral : 4.967 30.175 456 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 11.63 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.43), residues: 386 helix: 2.07 (0.32), residues: 255 sheet: None (None), residues: 0 loop : -0.70 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 243 HIS 0.006 0.001 HIS R 212 PHE 0.012 0.002 PHE R 280 TYR 0.028 0.002 TYR R 148 ARG 0.002 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.317 Fit side-chains REVERT: R 41 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6565 (mm-30) REVERT: R 201 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7017 (pt) REVERT: R 384 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7638 (mm) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.8337 time to fit residues: 23.7874 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3351 Z= 0.189 Angle : 0.538 9.853 4571 Z= 0.281 Chirality : 0.037 0.126 497 Planarity : 0.004 0.059 557 Dihedral : 4.826 30.880 456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.20 % Allowed : 12.50 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 386 helix: 2.31 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.68 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 243 HIS 0.003 0.001 HIS R 212 PHE 0.012 0.001 PHE R 280 TYR 0.025 0.002 TYR R 148 ARG 0.009 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 0.372 Fit side-chains REVERT: R 41 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6615 (mm-30) REVERT: R 201 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6879 (pt) REVERT: R 414 ARG cc_start: 0.6190 (mmt90) cc_final: 0.5188 (mmp-170) outliers start: 11 outliers final: 8 residues processed: 33 average time/residue: 0.6958 time to fit residues: 24.4130 Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3351 Z= 0.252 Angle : 0.574 10.498 4571 Z= 0.298 Chirality : 0.039 0.132 497 Planarity : 0.004 0.060 557 Dihedral : 4.900 29.842 456 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.49 % Allowed : 12.21 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.43), residues: 386 helix: 2.12 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.71 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 243 HIS 0.004 0.001 HIS R 180 PHE 0.013 0.002 PHE R 280 TYR 0.026 0.002 TYR R 148 ARG 0.005 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.345 Fit side-chains REVERT: R 41 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6689 (mm-30) REVERT: R 201 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6970 (pt) REVERT: R 384 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7649 (mm) outliers start: 12 outliers final: 8 residues processed: 34 average time/residue: 0.6846 time to fit residues: 24.7137 Evaluate side-chains 36 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 50.0000 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.166 Angle : 0.520 9.588 4571 Z= 0.269 Chirality : 0.037 0.125 497 Planarity : 0.004 0.059 557 Dihedral : 4.709 30.396 456 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 14.83 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.43), residues: 386 helix: 2.41 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.66 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 243 HIS 0.002 0.000 HIS R 212 PHE 0.012 0.001 PHE R 187 TYR 0.023 0.001 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.362 Fit side-chains REVERT: R 41 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6680 (mm-30) REVERT: R 201 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6851 (pt) REVERT: R 384 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7605 (mm) REVERT: R 397 MET cc_start: 0.7118 (mtt) cc_final: 0.6862 (mmp) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.7925 time to fit residues: 25.3174 Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3351 Z= 0.152 Angle : 0.499 9.229 4571 Z= 0.258 Chirality : 0.036 0.123 497 Planarity : 0.004 0.060 557 Dihedral : 4.558 29.915 456 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 15.41 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.43), residues: 386 helix: 2.57 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.65 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 PHE 0.011 0.001 PHE R 187 TYR 0.024 0.001 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.360 Fit side-chains REVERT: R 41 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6680 (mm-30) REVERT: R 384 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7558 (mm) REVERT: R 397 MET cc_start: 0.7088 (mtt) cc_final: 0.6840 (mmp) outliers start: 7 outliers final: 3 residues processed: 32 average time/residue: 0.8103 time to fit residues: 27.4851 Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 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: 0.7550 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3351 Z= 0.166 Angle : 0.498 7.244 4571 Z= 0.259 Chirality : 0.036 0.124 497 Planarity : 0.004 0.059 557 Dihedral : 4.577 30.496 456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.74 % Allowed : 15.99 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.43), residues: 386 helix: 2.58 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.55 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 243 HIS 0.002 0.000 HIS R 180 PHE 0.012 0.001 PHE R 187 TYR 0.024 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.322 Fit side-chains REVERT: R 41 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6672 (mm-30) REVERT: R 384 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (mm) REVERT: R 397 MET cc_start: 0.7099 (mtt) cc_final: 0.6845 (mmp) outliers start: 6 outliers final: 5 residues processed: 31 average time/residue: 0.8935 time to fit residues: 29.2374 Evaluate side-chains 32 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3351 Z= 0.144 Angle : 0.481 7.177 4571 Z= 0.250 Chirality : 0.036 0.120 497 Planarity : 0.004 0.059 557 Dihedral : 4.465 29.461 456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.74 % Allowed : 15.99 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.43), residues: 386 helix: 2.70 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.50 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.011 0.001 PHE R 187 TYR 0.024 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.382 Fit side-chains REVERT: R 41 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6668 (mm-30) REVERT: R 384 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7531 (mm) REVERT: R 397 MET cc_start: 0.7082 (mtt) cc_final: 0.6843 (mmp) outliers start: 6 outliers final: 5 residues processed: 31 average time/residue: 0.7318 time to fit residues: 24.1143 Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3351 Z= 0.137 Angle : 0.476 7.179 4571 Z= 0.247 Chirality : 0.035 0.119 497 Planarity : 0.004 0.059 557 Dihedral : 4.398 29.693 456 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.33 % Allowed : 15.41 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.43), residues: 386 helix: 2.79 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.54 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.011 0.001 PHE R 187 TYR 0.024 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.323 Fit side-chains REVERT: R 41 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6635 (mm-30) REVERT: R 384 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7509 (mm) REVERT: R 397 MET cc_start: 0.7086 (mtt) cc_final: 0.6863 (mmp) REVERT: R 414 ARG cc_start: 0.6135 (mmt90) cc_final: 0.5829 (mtt90) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.7190 time to fit residues: 25.1862 Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.204859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134889 restraints weight = 3242.826| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.09 r_work: 0.3376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3351 Z= 0.150 Angle : 0.487 7.184 4571 Z= 0.253 Chirality : 0.036 0.128 497 Planarity : 0.004 0.059 557 Dihedral : 4.413 29.640 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.74 % Allowed : 15.99 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.43), residues: 386 helix: 2.79 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.51 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.012 0.001 PHE R 187 TYR 0.024 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.32 seconds wall clock time: 24 minutes 37.48 seconds (1477.48 seconds total)