Starting phenix.real_space_refine on Mon Feb 10 23:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.map" model { file = "/net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ber_16009/02_2025/8ber_16009.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.079 sd= 0.328 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 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 4.31, per 1000 atoms: 1.30 Number of scatterers: 3309 At special positions: 0 Unit cell: (94.095, 70.848, 81.918, 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 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 307.9 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.882A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.664A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.573A pdb=" N LYS A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.190A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 47 through 73 Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.790A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 removed outlier: 4.230A pdb=" N THR B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 16 through 17 No H-bonds generated for 'chain 'C' and resid 16 through 17' Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.925A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 224 through 251 removed outlier: 5.207A pdb=" N LEU C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 221 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.78 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: 1029 1.34 - 1.46: 694 1.46 - 1.57: 1661 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CA ILE A 279 " pdb=" CB ILE A 279 " ideal model delta sigma weight residual 1.527 1.547 -0.021 1.31e-02 5.83e+03 2.45e+00 bond pdb=" CG MET C 64 " pdb=" SD MET C 64 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.45e+00 bond pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CG GLU C 257 " pdb=" CD GLU C 257 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4591 2.16 - 4.32: 63 4.32 - 6.48: 7 6.48 - 8.64: 0 8.64 - 10.79: 1 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C TYR A 272 " pdb=" N ARG A 273 " pdb=" CA ARG A 273 " ideal model delta sigma weight residual 120.49 131.28 -10.79 1.42e+00 4.96e-01 5.78e+01 angle pdb=" N GLU C 257 " pdb=" CA GLU C 257 " pdb=" CB GLU C 257 " ideal model delta sigma weight residual 110.28 116.61 -6.33 1.55e+00 4.16e-01 1.67e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.28 116.25 -5.97 1.55e+00 4.16e-01 1.49e+01 angle pdb=" C ILE C 256 " pdb=" N GLU C 257 " pdb=" CA GLU C 257 " ideal model delta sigma weight residual 120.31 115.08 5.23 1.52e+00 4.33e-01 1.18e+01 angle pdb=" C ASN C 232 " pdb=" N MET C 233 " pdb=" CA MET C 233 " ideal model delta sigma weight residual 122.23 117.61 4.62 1.57e+00 4.06e-01 8.64e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 1709 11.96 - 23.92: 200 23.92 - 35.88: 62 35.88 - 47.85: 22 47.85 - 59.81: 8 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ILE B 266 " pdb=" C ILE B 266 " pdb=" N ARG B 267 " pdb=" CA ARG B 267 " ideal model delta harmonic sigma weight residual 180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 123.36 -30.36 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ARG B 267 " pdb=" C ARG B 267 " pdb=" N THR B 268 " pdb=" CA THR B 268 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 452 0.056 - 0.112: 66 0.112 - 0.168: 4 0.168 - 0.224: 1 0.224 - 0.280: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 230 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ASN C 230 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN C 230 " -0.017 2.00e-02 2.50e+03 pdb=" N THR C 231 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 269 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO B 270 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 273 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 274 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 274 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 274 " -0.016 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 480 2.75 - 3.29: 3664 3.29 - 3.83: 5909 3.83 - 4.36: 6389 4.36 - 4.90: 10758 Nonbonded interactions: 27200 Sorted by model distance: nonbonded pdb=" O TYR C 228 " pdb=" ND2 ASN C 232 " model vdw 2.214 3.120 nonbonded pdb=" O VAL A 11 " pdb=" OG SER A 15 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASN C 230 " pdb=" N THR C 231 " model vdw 2.241 3.120 nonbonded pdb=" OE2 GLU A 6 " pdb=" NH1 ARG B 54 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A 229 " pdb=" N GLY A 234 " model vdw 2.284 3.120 ... (remaining 27195 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 5.360 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 0.031 3411 Z= 0.192 Angle : 0.613 10.795 4662 Z= 0.352 Chirality : 0.041 0.280 525 Planarity : 0.004 0.042 585 Dihedral : 12.678 59.807 1212 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 2.47 (0.44), residues: 402 helix: 1.88 (0.31), residues: 294 sheet: None (None), residues: 0 loop : 1.18 (0.68), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 60 HIS 0.002 0.001 HIS B 49 PHE 0.013 0.001 PHE B 237 TYR 0.006 0.001 TYR A 272 ARG 0.007 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.395 Fit side-chains REVERT: A 64 MET cc_start: 0.9413 (mmp) cc_final: 0.9174 (mmt) REVERT: A 233 MET cc_start: 0.9353 (mpp) cc_final: 0.9003 (mpp) REVERT: B 64 MET cc_start: 0.9228 (mmp) cc_final: 0.8838 (mmt) REVERT: B 233 MET cc_start: 0.9501 (pmm) cc_final: 0.9161 (pmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1423 time to fit residues: 3.9353 Evaluate side-chains 11 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.030388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027408 restraints weight = 58714.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.027980 restraints weight = 35814.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.028349 restraints weight = 24733.090| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.216 Angle : 0.615 6.822 4662 Z= 0.334 Chirality : 0.042 0.276 525 Planarity : 0.005 0.041 585 Dihedral : 4.589 21.601 447 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.43), residues: 402 helix: 1.98 (0.30), residues: 297 sheet: None (None), residues: 0 loop : 1.08 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 69 HIS 0.003 0.001 HIS B 45 PHE 0.017 0.001 PHE B 237 TYR 0.008 0.001 TYR C 272 ARG 0.004 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.408 Fit side-chains REVERT: B 64 MET cc_start: 0.9246 (mmp) cc_final: 0.8850 (mmt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1396 time to fit residues: 2.6239 Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.030228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.027306 restraints weight = 56850.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027843 restraints weight = 34824.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.028223 restraints weight = 24159.032| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3411 Z= 0.222 Angle : 0.623 9.393 4662 Z= 0.326 Chirality : 0.041 0.257 525 Planarity : 0.005 0.044 585 Dihedral : 4.644 21.922 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.55 % Allowed : 7.38 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.43), residues: 402 helix: 1.95 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 1.09 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 69 HIS 0.003 0.001 HIS B 45 PHE 0.011 0.001 PHE B 237 TYR 0.011 0.001 TYR B 228 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9228 (mmp) cc_final: 0.8790 (mmt) REVERT: C 253 GLU cc_start: 0.9330 (pm20) cc_final: 0.9014 (pm20) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.1376 time to fit residues: 2.8639 Evaluate side-chains 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.029973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.026972 restraints weight = 58395.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027523 restraints weight = 35366.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.027904 restraints weight = 24446.741| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3411 Z= 0.235 Angle : 0.651 9.501 4662 Z= 0.340 Chirality : 0.041 0.247 525 Planarity : 0.005 0.043 585 Dihedral : 4.673 22.270 447 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 9.84 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.43), residues: 402 helix: 1.91 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.12 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 60 HIS 0.003 0.001 HIS B 45 PHE 0.009 0.001 PHE A 21 TYR 0.012 0.001 TYR B 228 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.402 Fit side-chains REVERT: B 64 MET cc_start: 0.9257 (mmp) cc_final: 0.8843 (mmt) REVERT: C 253 GLU cc_start: 0.9372 (pm20) cc_final: 0.9110 (pm20) outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 0.1321 time to fit residues: 2.8140 Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.030021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.027121 restraints weight = 57566.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027672 restraints weight = 34410.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.028046 restraints weight = 23499.425| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3411 Z= 0.254 Angle : 0.664 9.967 4662 Z= 0.345 Chirality : 0.041 0.246 525 Planarity : 0.005 0.043 585 Dihedral : 4.707 22.699 447 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.09 % Allowed : 10.38 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.43), residues: 402 helix: 1.93 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.10 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 69 HIS 0.003 0.001 HIS B 45 PHE 0.010 0.001 PHE C 237 TYR 0.012 0.001 TYR B 228 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.379 Fit side-chains REVERT: B 64 MET cc_start: 0.9304 (mmp) cc_final: 0.8885 (mmt) REVERT: C 63 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9429 (tp) outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.1341 time to fit residues: 3.0148 Evaluate side-chains 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.029900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.026968 restraints weight = 59872.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.027536 restraints weight = 35257.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.027929 restraints weight = 23822.949| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3411 Z= 0.233 Angle : 0.613 9.546 4662 Z= 0.324 Chirality : 0.040 0.240 525 Planarity : 0.005 0.042 585 Dihedral : 4.704 22.949 447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 12.02 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.44), residues: 402 helix: 1.99 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.11 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 69 HIS 0.002 0.001 HIS C 45 PHE 0.009 0.001 PHE A 21 TYR 0.011 0.001 TYR B 228 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9334 (mmp) cc_final: 0.8892 (mmt) outliers start: 3 outliers final: 1 residues processed: 14 average time/residue: 0.1381 time to fit residues: 2.9151 Evaluate side-chains 11 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.029966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.027064 restraints weight = 58344.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027627 restraints weight = 34419.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.028014 restraints weight = 23247.703| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3411 Z= 0.225 Angle : 0.612 8.238 4662 Z= 0.323 Chirality : 0.040 0.235 525 Planarity : 0.005 0.042 585 Dihedral : 4.637 22.962 447 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.55 % Allowed : 13.66 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.44), residues: 402 helix: 2.05 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.16 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 69 HIS 0.002 0.001 HIS C 45 PHE 0.008 0.001 PHE C 237 TYR 0.012 0.001 TYR B 228 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9227 (mmm) cc_final: 0.8932 (mmt) REVERT: B 64 MET cc_start: 0.9351 (mmp) cc_final: 0.8914 (mmt) outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.1367 time to fit residues: 2.5725 Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.029995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.027093 restraints weight = 58051.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.027648 restraints weight = 34574.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.028027 restraints weight = 23543.565| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3411 Z= 0.198 Angle : 0.592 7.521 4662 Z= 0.309 Chirality : 0.039 0.221 525 Planarity : 0.004 0.041 585 Dihedral : 4.545 22.508 447 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.09 % Allowed : 13.11 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.44), residues: 402 helix: 2.08 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.19 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.002 0.001 HIS C 45 PHE 0.008 0.001 PHE C 16 TYR 0.014 0.001 TYR B 228 ARG 0.002 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9170 (mmm) cc_final: 0.8833 (mmm) REVERT: B 64 MET cc_start: 0.9368 (mmp) cc_final: 0.8906 (mmt) outliers start: 4 outliers final: 3 residues processed: 14 average time/residue: 0.1428 time to fit residues: 2.9851 Evaluate side-chains 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.029928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.026984 restraints weight = 58429.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027546 restraints weight = 35008.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027934 restraints weight = 23977.357| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3411 Z= 0.207 Angle : 0.624 7.614 4662 Z= 0.327 Chirality : 0.039 0.225 525 Planarity : 0.004 0.041 585 Dihedral : 4.519 22.334 447 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 14.21 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.44), residues: 402 helix: 2.05 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.19 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.003 0.001 HIS C 45 PHE 0.008 0.001 PHE C 237 TYR 0.012 0.001 TYR B 228 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9210 (mmm) cc_final: 0.8865 (mmm) REVERT: B 64 MET cc_start: 0.9375 (mmp) cc_final: 0.8939 (mmt) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.1325 time to fit residues: 2.6409 Evaluate side-chains 12 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.029997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.027025 restraints weight = 57619.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.027572 restraints weight = 34944.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027953 restraints weight = 24129.861| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3411 Z= 0.175 Angle : 0.610 7.969 4662 Z= 0.317 Chirality : 0.039 0.216 525 Planarity : 0.004 0.041 585 Dihedral : 4.411 21.775 447 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 13.93 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.44), residues: 402 helix: 2.09 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.26 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 265 HIS 0.002 0.001 HIS A 244 PHE 0.007 0.001 PHE C 16 TYR 0.011 0.001 TYR B 228 ARG 0.002 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9202 (mmm) cc_final: 0.8954 (mmt) REVERT: B 64 MET cc_start: 0.9391 (mmp) cc_final: 0.8930 (mmt) outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.1537 time to fit residues: 3.1475 Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 overall best weight: 3.7796 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.030176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.027207 restraints weight = 57432.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.027757 restraints weight = 35122.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.028137 restraints weight = 24321.299| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3411 Z= 0.170 Angle : 0.614 9.737 4662 Z= 0.315 Chirality : 0.038 0.208 525 Planarity : 0.004 0.040 585 Dihedral : 4.285 21.043 447 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 13.93 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.44), residues: 402 helix: 2.09 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.33 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 265 HIS 0.002 0.001 HIS C 45 PHE 0.007 0.001 PHE C 16 TYR 0.011 0.001 TYR B 228 ARG 0.002 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1153.63 seconds wall clock time: 21 minutes 41.50 seconds (1301.50 seconds total)