Starting phenix.real_space_refine on Fri Dec 27 04:41:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.map" model { file = "/net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zsd_14930/12_2024/7zsd_14930.cif" } resolution = 3.29 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= 0.019 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 9 5.16 5 C 1363 2.51 5 N 362 2.21 5 O 386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2120 Number of models: 1 Model: "" Number of chains: 3 Chain: "M" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1573 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "P" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.39, per 1000 atoms: 1.13 Number of scatterers: 2120 At special positions: 0 Unit cell: (77.7546, 60.4758, 70.3494, 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 9 16.00 O 386 8.00 N 362 7.00 C 1363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.03 Simple disulfide: pdb=" SG CYS M 391 " - pdb=" SG CYS M 525 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN M 343 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 264.4 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 33.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'M' and resid 337 through 343 Processing helix chain 'M' and resid 349 through 353 Processing helix chain 'M' and resid 365 through 371 removed outlier: 3.735A pdb=" N TYR M 369 " --> pdb=" O TYR M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 405 through 410 removed outlier: 4.645A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'P' and resid 3 through 24 Processing helix chain 'P' and resid 26 through 49 removed outlier: 3.633A pdb=" N ALA P 30 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL M 395 " --> pdb=" O ILE M 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 452 through 454 76 hydrogen bonds defined for protein. 210 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: 0.48 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 676 1.34 - 1.46: 533 1.46 - 1.58: 960 1.58 - 1.70: 0 1.70 - 1.81: 10 Bond restraints: 2179 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C3 NAG A 1 " pdb=" O3 NAG A 1 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 2174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2863 1.44 - 2.88: 75 2.88 - 4.32: 16 4.32 - 5.76: 2 5.76 - 7.20: 3 Bond angle restraints: 2959 Sorted by residual: angle pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " pdb=" CD LYS M 444 " ideal model delta sigma weight residual 111.30 117.10 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU M 390 " pdb=" CB LEU M 390 " pdb=" CG LEU M 390 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LYS M 444 " pdb=" CB LYS M 444 " pdb=" CG LYS M 444 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.22e+00 angle pdb=" C THR P 1 " pdb=" N ASN P 2 " pdb=" CA ASN P 2 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 angle pdb=" CB GLU M 465 " pdb=" CG GLU M 465 " pdb=" CD GLU M 465 " ideal model delta sigma weight residual 112.60 115.67 -3.07 1.70e+00 3.46e-01 3.26e+00 ... (remaining 2954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 1206 21.64 - 43.29: 88 43.29 - 64.93: 13 64.93 - 86.58: 11 86.58 - 108.22: 5 Dihedral angle restraints: 1323 sinusoidal: 559 harmonic: 764 Sorted by residual: dihedral pdb=" CB CYS M 391 " pdb=" SG CYS M 391 " pdb=" SG CYS M 525 " pdb=" CB CYS M 525 " ideal model delta sinusoidal sigma weight residual -86.00 -143.35 57.35 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CB CYS M 480 " pdb=" SG CYS M 480 " pdb=" SG CYS M 488 " pdb=" CB CYS M 488 " ideal model delta sinusoidal sigma weight residual -86.00 -125.54 39.54 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" C2 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" C4 NAG A 1 " pdb=" C5 NAG A 1 " ideal model delta sinusoidal sigma weight residual 53.78 -54.44 108.22 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 1320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 252 0.056 - 0.111: 58 0.111 - 0.167: 3 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 314 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE M 402 " pdb=" N ILE M 402 " pdb=" C ILE M 402 " pdb=" CB ILE M 402 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE M 434 " pdb=" N ILE M 434 " pdb=" C ILE M 434 " pdb=" CB ILE M 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 311 not shown) Planarity restraints: 387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 53 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO P 54 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO P 54 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 54 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 40 " 0.007 2.00e-02 2.50e+03 7.37e-03 1.09e+00 pdb=" CG TYR P 40 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR P 40 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR P 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR P 40 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR P 40 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR P 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 334 " -0.004 2.00e-02 2.50e+03 7.69e-03 5.91e-01 pdb=" C ASN M 334 " 0.013 2.00e-02 2.50e+03 pdb=" O ASN M 334 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU M 335 " -0.004 2.00e-02 2.50e+03 ... (remaining 384 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 338 2.76 - 3.30: 2127 3.30 - 3.83: 3418 3.83 - 4.37: 3929 4.37 - 4.90: 6641 Nonbonded interactions: 16453 Sorted by model distance: nonbonded pdb=" O ARG P 35 " pdb=" NE2 GLN P 39 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP M 398 " pdb=" OH TYR M 423 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASN M 487 " pdb=" OH TYR M 489 " model vdw 2.299 3.040 nonbonded pdb=" O LEU M 518 " pdb=" ND1 HIS M 519 " model vdw 2.308 3.120 nonbonded pdb=" ND2 ASN M 439 " pdb=" OE1 GLN M 506 " model vdw 2.360 3.120 ... (remaining 16448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.003 0.035 2179 Z= 0.208 Angle : 0.598 7.202 2959 Z= 0.295 Chirality : 0.046 0.278 314 Planarity : 0.003 0.031 386 Dihedral : 17.984 108.222 825 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.53), residues: 257 helix: 0.40 (0.56), residues: 89 sheet: 0.67 (0.79), residues: 42 loop : -0.57 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 353 HIS 0.003 0.001 HIS M 519 PHE 0.011 0.001 PHE M 377 TYR 0.017 0.002 TYR P 40 ARG 0.003 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1765 time to fit residues: 8.9469 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2179 Z= 0.260 Angle : 0.639 8.546 2959 Z= 0.311 Chirality : 0.048 0.242 314 Planarity : 0.004 0.024 386 Dihedral : 15.008 88.122 336 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.90 % Allowed : 11.21 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.53), residues: 257 helix: 0.46 (0.57), residues: 88 sheet: 0.73 (0.86), residues: 34 loop : -0.80 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 436 HIS 0.005 0.002 HIS M 519 PHE 0.010 0.002 PHE M 377 TYR 0.014 0.002 TYR P 55 ARG 0.004 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.229 Fit side-chains REVERT: M 430 THR cc_start: 0.8517 (p) cc_final: 0.8285 (p) REVERT: P 5 GLU cc_start: 0.6596 (mp0) cc_final: 0.6395 (mp0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1561 time to fit residues: 6.8627 Evaluate side-chains 32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 overall best weight: 0.2412 ------------------------------------------------------------------------------- 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: 0.7388 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2179 Z= 0.155 Angle : 0.574 6.637 2959 Z= 0.281 Chirality : 0.046 0.220 314 Planarity : 0.003 0.020 386 Dihedral : 13.415 77.357 336 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.35 % Allowed : 11.21 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.53), residues: 257 helix: 0.30 (0.57), residues: 88 sheet: 1.21 (0.90), residues: 32 loop : -0.86 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.007 0.001 PHE M 497 TYR 0.016 0.001 TYR P 47 ARG 0.005 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: P 5 GLU cc_start: 0.6770 (mp0) cc_final: 0.6509 (mp0) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.1433 time to fit residues: 7.6229 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- 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: 0.7554 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2179 Z= 0.310 Angle : 0.665 7.090 2959 Z= 0.321 Chirality : 0.050 0.292 314 Planarity : 0.004 0.025 386 Dihedral : 11.801 64.707 336 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.48 % Allowed : 12.11 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.52), residues: 257 helix: 0.29 (0.56), residues: 88 sheet: 0.61 (0.89), residues: 32 loop : -1.11 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.009 0.001 PHE M 375 TYR 0.017 0.002 TYR P 47 ARG 0.006 0.001 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8618 (p) cc_final: 0.8367 (p) REVERT: P 5 GLU cc_start: 0.6752 (mp0) cc_final: 0.6404 (mp0) outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 0.1581 time to fit residues: 7.9418 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 375 PHE Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 511 VAL Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2179 Z= 0.228 Angle : 0.626 7.133 2959 Z= 0.304 Chirality : 0.048 0.304 314 Planarity : 0.004 0.025 386 Dihedral : 10.996 59.659 336 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.04 % Allowed : 14.80 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.52), residues: 257 helix: 0.38 (0.57), residues: 88 sheet: -0.51 (0.76), residues: 42 loop : -0.92 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.012 0.001 PHE M 374 TYR 0.013 0.002 TYR P 47 ARG 0.007 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8536 (p) cc_final: 0.8278 (p) REVERT: P 5 GLU cc_start: 0.6724 (mp0) cc_final: 0.6366 (mp0) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.1453 time to fit residues: 7.0679 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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: 0.7459 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2179 Z= 0.180 Angle : 0.627 7.233 2959 Z= 0.300 Chirality : 0.047 0.293 314 Planarity : 0.004 0.024 386 Dihedral : 10.414 56.880 336 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 16.14 % Favored : 80.27 % 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: -0.30 (0.53), residues: 257 helix: 0.44 (0.58), residues: 88 sheet: 0.86 (0.89), residues: 32 loop : -0.88 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.007 0.001 PHE M 374 TYR 0.013 0.001 TYR M 495 ARG 0.005 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.1277 time to fit residues: 6.4072 Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2179 Z= 0.226 Angle : 0.632 7.108 2959 Z= 0.307 Chirality : 0.048 0.315 314 Planarity : 0.004 0.024 386 Dihedral : 10.047 53.985 336 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 15.70 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.53), residues: 257 helix: 0.45 (0.57), residues: 88 sheet: -0.37 (0.77), residues: 42 loop : -0.92 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.006 0.001 PHE M 375 TYR 0.020 0.002 TYR P 47 ARG 0.004 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: M 430 THR cc_start: 0.8494 (p) cc_final: 0.8222 (p) REVERT: P 5 GLU cc_start: 0.6611 (mp0) cc_final: 0.6175 (mp0) outliers start: 8 outliers final: 8 residues processed: 38 average time/residue: 0.1283 time to fit residues: 6.0317 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 2.9990 overall best weight: 0.3522 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2179 Z= 0.186 Angle : 0.639 7.115 2959 Z= 0.307 Chirality : 0.047 0.302 314 Planarity : 0.003 0.023 386 Dihedral : 9.700 51.091 336 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 16.14 % Favored : 80.27 % 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: -0.35 (0.53), residues: 257 helix: 0.48 (0.58), residues: 88 sheet: 0.53 (0.87), residues: 32 loop : -0.88 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.007 0.003 HIS M 519 PHE 0.006 0.001 PHE M 497 TYR 0.015 0.001 TYR P 47 ARG 0.004 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: P 5 GLU cc_start: 0.6779 (mp0) cc_final: 0.6427 (mp0) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.1572 time to fit residues: 7.0672 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2179 Z= 0.205 Angle : 0.648 6.983 2959 Z= 0.314 Chirality : 0.047 0.310 314 Planarity : 0.004 0.023 386 Dihedral : 9.419 48.963 336 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 16.59 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.53), residues: 257 helix: 0.48 (0.58), residues: 88 sheet: 0.40 (0.87), residues: 32 loop : -0.87 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.005 0.001 PHE M 497 TYR 0.015 0.001 TYR P 47 ARG 0.008 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 5 GLU cc_start: 0.6791 (mp0) cc_final: 0.6428 (mp0) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1386 time to fit residues: 6.0790 Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2179 Z= 0.225 Angle : 0.668 7.016 2959 Z= 0.321 Chirality : 0.048 0.322 314 Planarity : 0.004 0.028 386 Dihedral : 9.332 47.784 336 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 15.70 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.52), residues: 257 helix: 0.39 (0.57), residues: 88 sheet: -0.60 (0.76), residues: 42 loop : -0.81 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.006 0.001 PHE M 375 TYR 0.019 0.002 TYR M 495 ARG 0.009 0.000 ARG P 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 5 GLU cc_start: 0.6762 (mp0) cc_final: 0.6377 (mp0) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.1341 time to fit residues: 6.1691 Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 492 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 515 PHE Chi-restraints excluded: chain M residue 525 CYS Chi-restraints excluded: chain P residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.126067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108324 restraints weight = 5012.724| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.03 r_work: 0.3573 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2179 Z= 0.201 Angle : 0.657 7.058 2959 Z= 0.318 Chirality : 0.047 0.308 314 Planarity : 0.004 0.026 386 Dihedral : 9.070 45.796 336 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 16.59 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.52), residues: 257 helix: 0.47 (0.58), residues: 88 sheet: 0.37 (0.85), residues: 32 loop : -0.88 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 353 HIS 0.005 0.002 HIS M 519 PHE 0.007 0.001 PHE M 497 TYR 0.016 0.001 TYR P 47 ARG 0.009 0.000 ARG P 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1023.64 seconds wall clock time: 19 minutes 37.32 seconds (1177.32 seconds total)