Starting phenix.real_space_refine on Mon Feb 10 20:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zsd_14930/02_2025/7zsd_14930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zsd_14930/02_2025/7zsd_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_14930/02_2025/7zsd_14930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zsd_14930/02_2025/7zsd_14930.map" model { file = "/net/cci-nas-00/data/ceres_data/7zsd_14930/02_2025/7zsd_14930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zsd_14930/02_2025/7zsd_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-5592/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: 3.32, per 1000 atoms: 1.57 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: 0.64 Conformation dependent library (CDL) restraints added in 279.1 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: 0.58 Time building geometry restraints manager: 0.76 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: 1.200 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.920 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- 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 : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1843 time to fit residues: 9.3265 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 : 0.299 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.126458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108941 restraints weight = 5032.538| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.00 r_work: 0.3612 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.247 Fit side-chains REVERT: M 430 THR cc_start: 0.8834 (p) cc_final: 0.8597 (p) REVERT: M 465 GLU cc_start: 0.5381 (tp30) cc_final: 0.5114 (tp30) REVERT: M 495 TYR cc_start: 0.7592 (m-80) cc_final: 0.7392 (m-80) REVERT: P 5 GLU cc_start: 0.6830 (mp0) cc_final: 0.6550 (mp0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1515 time to fit residues: 6.6322 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 : 0.256 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.124812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106502 restraints weight = 5027.015| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.07 r_work: 0.3550 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2179 Z= 0.195 Angle : 0.583 6.450 2959 Z= 0.287 Chirality : 0.047 0.238 314 Planarity : 0.004 0.022 386 Dihedral : 13.821 80.021 336 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.35 % Allowed : 12.11 % Favored : 86.55 % 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: 0.33 (0.57), residues: 88 sheet: 1.04 (0.90), residues: 32 loop : -0.94 (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 0.006 0.001 PHE M 497 TYR 0.015 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 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: M 392 PHE cc_start: 0.7634 (m-80) cc_final: 0.7287 (m-80) REVERT: M 430 THR cc_start: 0.8827 (p) cc_final: 0.8559 (p) REVERT: M 518 LEU cc_start: 0.6441 (tp) cc_final: 0.6212 (tt) REVERT: P 5 GLU cc_start: 0.6787 (mp0) cc_final: 0.6387 (mp0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1492 time to fit residues: 6.9707 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 492 LEU 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 16 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.126956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.109024 restraints weight = 4930.871| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.02 r_work: 0.3589 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2179 Z= 0.168 Angle : 0.586 6.943 2959 Z= 0.284 Chirality : 0.047 0.240 314 Planarity : 0.003 0.021 386 Dihedral : 12.051 67.661 336 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.59 % Allowed : 12.11 % 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: -0.39 (0.53), residues: 257 helix: 0.38 (0.57), residues: 88 sheet: 0.92 (0.89), residues: 32 loop : -0.97 (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 0.011 0.001 TYR P 40 ARG 0.006 0.000 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 49 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8120 (m-80) cc_final: 0.7767 (m-80) REVERT: M 392 PHE cc_start: 0.7610 (m-80) cc_final: 0.7234 (m-80) REVERT: M 406 GLU cc_start: 0.8499 (pt0) cc_final: 0.8258 (pm20) REVERT: M 465 GLU cc_start: 0.4264 (tp30) cc_final: 0.4000 (tp30) REVERT: M 495 TYR cc_start: 0.7579 (m-80) cc_final: 0.7364 (m-80) REVERT: P 5 GLU cc_start: 0.7146 (mp0) cc_final: 0.6761 (mp0) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.1341 time to fit residues: 7.3966 Evaluate side-chains 41 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 VAL Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 500 THR 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 15 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.125766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107769 restraints weight = 5096.882| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.05 r_work: 0.3565 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1990 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= 0.195 Angle : 0.625 7.359 2959 Z= 0.297 Chirality : 0.047 0.297 314 Planarity : 0.003 0.022 386 Dihedral : 10.649 58.984 336 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.59 % Allowed : 14.35 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.52), residues: 257 helix: 0.43 (0.57), residues: 88 sheet: 0.83 (0.89), residues: 32 loop : -0.98 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.013 0.001 PHE M 374 TYR 0.010 0.001 TYR P 40 ARG 0.004 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 46 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8115 (m-80) cc_final: 0.7704 (m-80) REVERT: M 392 PHE cc_start: 0.7651 (m-80) cc_final: 0.7241 (m-80) REVERT: M 465 GLU cc_start: 0.4276 (tp30) cc_final: 0.4028 (tp30) REVERT: M 495 TYR cc_start: 0.7552 (m-80) cc_final: 0.7337 (m-80) REVERT: P 5 GLU cc_start: 0.7038 (mp0) cc_final: 0.6614 (mp0) outliers start: 8 outliers final: 8 residues processed: 43 average time/residue: 0.1356 time to fit residues: 6.8896 Evaluate side-chains 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.5472 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.126643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108704 restraints weight = 5000.156| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.07 r_work: 0.3583 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2160 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= 0.175 Angle : 0.602 7.239 2959 Z= 0.289 Chirality : 0.047 0.288 314 Planarity : 0.004 0.022 386 Dihedral : 10.165 55.498 336 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 15.25 % 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: -0.29 (0.53), residues: 257 helix: 0.51 (0.58), residues: 88 sheet: 0.79 (0.87), residues: 32 loop : -0.89 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.005 0.001 PHE M 374 TYR 0.009 0.001 TYR P 40 ARG 0.006 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 48 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8853 (m) REVERT: M 365 TYR cc_start: 0.8065 (m-80) cc_final: 0.7697 (m-80) REVERT: M 392 PHE cc_start: 0.7762 (m-80) cc_final: 0.7444 (m-80) REVERT: M 465 GLU cc_start: 0.3796 (tp30) cc_final: 0.3521 (tp30) REVERT: M 495 TYR cc_start: 0.7583 (m-80) cc_final: 0.7324 (m-80) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.1446 time to fit residues: 7.5751 Evaluate side-chains 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.125560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107734 restraints weight = 5128.981| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.03 r_work: 0.3561 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2179 Z= 0.201 Angle : 0.631 7.060 2959 Z= 0.303 Chirality : 0.047 0.308 314 Planarity : 0.004 0.023 386 Dihedral : 9.754 52.204 336 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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: -0.47 (0.53), residues: 257 helix: 0.48 (0.58), residues: 88 sheet: -0.38 (0.76), residues: 42 loop : -0.79 (0.56), residues: 127 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 0.006 0.001 PHE M 374 TYR 0.021 0.001 TYR P 47 ARG 0.006 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 44 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 365 TYR cc_start: 0.8066 (m-80) cc_final: 0.7768 (m-80) REVERT: M 392 PHE cc_start: 0.7752 (m-80) cc_final: 0.7542 (m-80) REVERT: M 465 GLU cc_start: 0.3851 (tp30) cc_final: 0.3575 (tp30) REVERT: M 495 TYR cc_start: 0.7563 (m-80) cc_final: 0.7305 (m-80) REVERT: P 5 GLU cc_start: 0.7048 (mp0) cc_final: 0.6714 (mp0) outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.1272 time to fit residues: 6.2412 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 : 0.244 ------------------------------------------------------------------------------- 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 15 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109028 restraints weight = 5191.801| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.08 r_work: 0.3586 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2179 Z= 0.181 Angle : 0.620 7.036 2959 Z= 0.298 Chirality : 0.047 0.301 314 Planarity : 0.004 0.022 386 Dihedral : 9.449 49.623 336 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.19 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: -0.28 (0.53), residues: 257 helix: 0.54 (0.58), residues: 88 sheet: 0.56 (0.85), residues: 32 loop : -0.83 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.006 0.002 HIS M 519 PHE 0.005 0.001 PHE M 497 TYR 0.016 0.001 TYR P 47 ARG 0.005 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 45 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8872 (m) REVERT: M 365 TYR cc_start: 0.8045 (m-80) cc_final: 0.7687 (m-80) REVERT: M 392 PHE cc_start: 0.7794 (m-80) cc_final: 0.7578 (m-80) REVERT: M 465 GLU cc_start: 0.3758 (tp30) cc_final: 0.3512 (tp30) REVERT: M 495 TYR cc_start: 0.7568 (m-80) cc_final: 0.7321 (m-80) REVERT: P 5 GLU cc_start: 0.7028 (mp0) cc_final: 0.6667 (mp0) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.1436 time to fit residues: 7.1283 Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 18 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.125234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107507 restraints weight = 5119.136| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.05 r_work: 0.3556 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2179 Z= 0.215 Angle : 0.650 6.934 2959 Z= 0.311 Chirality : 0.047 0.311 314 Planarity : 0.004 0.026 386 Dihedral : 9.327 48.442 336 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 15.25 % 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: -0.49 (0.53), residues: 257 helix: 0.48 (0.58), residues: 88 sheet: -0.53 (0.74), residues: 42 loop : -0.75 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 353 HIS 0.005 0.001 HIS M 519 PHE 0.006 0.001 PHE M 375 TYR 0.016 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 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8883 (m) REVERT: M 365 TYR cc_start: 0.8075 (m-80) cc_final: 0.7779 (m-80) REVERT: M 465 GLU cc_start: 0.3842 (tp30) cc_final: 0.3572 (tp30) REVERT: M 495 TYR cc_start: 0.7608 (m-80) cc_final: 0.7318 (m-80) REVERT: P 5 GLU cc_start: 0.7010 (mp0) cc_final: 0.6632 (mp0) outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.1240 time to fit residues: 6.0419 Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.126268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108820 restraints weight = 5097.679| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.99 r_work: 0.3579 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2179 Z= 0.193 Angle : 0.656 7.926 2959 Z= 0.311 Chirality : 0.047 0.304 314 Planarity : 0.004 0.028 386 Dihedral : 9.143 46.615 336 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.39 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: -0.28 (0.52), residues: 257 helix: 0.52 (0.58), residues: 88 sheet: 0.46 (0.85), residues: 32 loop : -0.79 (0.54), 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 0.005 0.001 PHE M 497 TYR 0.016 0.001 TYR P 47 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 43 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 362 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8903 (m) REVERT: M 465 GLU cc_start: 0.3904 (tp30) cc_final: 0.3657 (tp30) REVERT: M 495 TYR cc_start: 0.7444 (m-80) cc_final: 0.7210 (m-80) REVERT: P 5 GLU cc_start: 0.7019 (mp0) cc_final: 0.6632 (mp0) outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.1102 time to fit residues: 5.3778 Evaluate side-chains 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.124832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107193 restraints weight = 5035.053| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.00 r_work: 0.3562 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2179 Z= 0.215 Angle : 0.643 6.814 2959 Z= 0.310 Chirality : 0.047 0.317 314 Planarity : 0.004 0.026 386 Dihedral : 9.123 46.102 336 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.62 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: -0.46 (0.53), residues: 257 helix: 0.50 (0.58), residues: 88 sheet: -0.55 (0.74), residues: 42 loop : -0.72 (0.57), residues: 127 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 0.006 0.001 PHE M 392 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: 1494.55 seconds wall clock time: 27 minutes 16.53 seconds (1636.53 seconds total)