Starting phenix.real_space_refine on Wed Mar 5 18:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ber_16009/03_2025/8ber_16009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ber_16009/03_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_16009/03_2025/8ber_16009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ber_16009/03_2025/8ber_16009.map" model { file = "/net/cci-nas-00/data/ceres_data/8ber_16009/03_2025/8ber_16009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ber_16009/03_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-5624/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: 3.44, per 1000 atoms: 1.04 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: 0.86 Conformation dependent library (CDL) restraints added in 393.3 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: 0.29 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: 0.87 Time building geometry restraints manager: 1.02 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: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- 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 : 0.358 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: 0.1335 time to fit residues: 3.7447 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 : 0.360 ------------------------------------------------------------------------------- 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 = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027408 restraints weight = 58714.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.027977 restraints weight = 35810.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.028353 restraints weight = 24782.703| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.398 Fit side-chains REVERT: B 64 MET cc_start: 0.9242 (mmp) cc_final: 0.8847 (mmt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1357 time to fit residues: 2.5585 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 : 0.401 ------------------------------------------------------------------------------- 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: 8.9990 chunk 10 optimal weight: 9.9990 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: 4.9990 chunk 23 optimal weight: 7.9990 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 = 0.3135 r_free = 0.3135 target = 0.030252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.027317 restraints weight = 57038.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.027865 restraints weight = 34772.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.028232 restraints weight = 24010.584| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1126 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= 0.213 Angle : 0.617 8.776 4662 Z= 0.323 Chirality : 0.041 0.253 525 Planarity : 0.005 0.044 585 Dihedral : 4.633 21.854 447 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.19 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 : 1.10 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 : 0.392 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9248 (mmp) cc_final: 0.8799 (mmt) REVERT: C 253 GLU cc_start: 0.9343 (pm20) cc_final: 0.9035 (pm20) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.1314 time to fit residues: 2.8754 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 : 0.417 ------------------------------------------------------------------------------- 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: 20.0000 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.029955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.027021 restraints weight = 58785.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.027566 restraints weight = 35298.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.027948 restraints weight = 24173.680| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3411 Z= 0.266 Angle : 0.665 9.793 4662 Z= 0.348 Chirality : 0.042 0.258 525 Planarity : 0.005 0.043 585 Dihedral : 4.694 22.376 447 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.55 % Allowed : 10.11 % Favored : 89.34 % 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 (0.43), residues: 402 helix: 1.90 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.08 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 60 HIS 0.003 0.001 HIS B 45 PHE 0.010 0.001 PHE A 21 TYR 0.011 0.001 TYR B 228 ARG 0.003 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 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.359 Fit side-chains REVERT: B 64 MET cc_start: 0.9258 (mmp) cc_final: 0.8836 (mmt) outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 0.1223 time to fit residues: 2.4830 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 : 0.391 ------------------------------------------------------------------------------- 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: 20.0000 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.030020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.027119 restraints weight = 57504.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027672 restraints weight = 34312.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.028049 restraints weight = 23374.527| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3411 Z= 0.236 Angle : 0.655 9.944 4662 Z= 0.340 Chirality : 0.041 0.244 525 Planarity : 0.005 0.042 585 Dihedral : 4.697 22.723 447 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.82 % Allowed : 10.66 % 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: 2.55 (0.44), residues: 402 helix: 1.95 (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 0.002 0.001 HIS B 45 PHE 0.009 0.001 PHE C 237 TYR 0.011 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 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.370 Fit side-chains REVERT: B 64 MET cc_start: 0.9291 (mmp) cc_final: 0.8869 (mmt) outliers start: 3 outliers final: 0 residues processed: 14 average time/residue: 0.1366 time to fit residues: 2.9894 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 : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 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 = 0.3109 r_free = 0.3109 target = 0.029908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.026979 restraints weight = 59591.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.027536 restraints weight = 35125.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.027919 restraints weight = 23772.851| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3411 Z= 0.238 Angle : 0.649 12.785 4662 Z= 0.332 Chirality : 0.040 0.241 525 Planarity : 0.005 0.042 585 Dihedral : 4.702 22.904 447 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 2.65 (0.44), residues: 402 helix: 2.03 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.13 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 69 HIS 0.002 0.001 HIS C 45 PHE 0.009 0.001 PHE C 237 TYR 0.012 0.001 TYR B 228 ARG 0.003 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 : 0.411 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9329 (mmp) cc_final: 0.8889 (mmt) outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.1393 time to fit residues: 2.9994 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 : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 232 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- 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 = 0.030063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.027135 restraints weight = 57905.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027705 restraints weight = 34185.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.028081 restraints weight = 23111.167| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1991 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= 0.205 Angle : 0.613 10.425 4662 Z= 0.323 Chirality : 0.040 0.228 525 Planarity : 0.004 0.042 585 Dihedral : 4.649 22.763 447 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.09 % Allowed : 13.39 % Favored : 85.52 % 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: 2.65 (0.44), residues: 402 helix: 2.01 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.21 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.002 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 15 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9246 (mmm) cc_final: 0.8947 (mmm) REVERT: B 64 MET cc_start: 0.9347 (mmp) cc_final: 0.8930 (mmp) outliers start: 4 outliers final: 3 residues processed: 15 average time/residue: 0.1388 time to fit residues: 3.1980 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 232 ASN 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: 6.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.030021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.027100 restraints weight = 58011.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.027662 restraints weight = 34345.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.028029 restraints weight = 23282.051| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2158 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= 0.249 Angle : 0.661 12.706 4662 Z= 0.343 Chirality : 0.041 0.241 525 Planarity : 0.005 0.041 585 Dihedral : 4.677 22.835 447 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.09 % Allowed : 12.57 % Favored : 86.34 % 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: 2.61 (0.44), residues: 402 helix: 1.99 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.18 (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 0.010 0.001 PHE C 237 TYR 0.011 0.002 TYR B 228 ARG 0.003 0.000 ARG B 54 *********************** 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 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9190 (mmm) cc_final: 0.8880 (mmt) REVERT: B 64 MET cc_start: 0.9371 (mmp) cc_final: 0.8905 (mmt) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.1261 time to fit residues: 2.5188 Evaluate side-chains 14 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 232 ASN 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: 7.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 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 = 0.3118 r_free = 0.3118 target = 0.029978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.026994 restraints weight = 58293.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.027556 restraints weight = 34971.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.027940 restraints weight = 23987.961| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2281 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= 0.217 Angle : 0.656 11.665 4662 Z= 0.339 Chirality : 0.040 0.228 525 Planarity : 0.004 0.041 585 Dihedral : 4.635 22.831 447 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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: 2.63 (0.44), residues: 402 helix: 2.00 (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 0.004 0.001 HIS C 45 PHE 0.008 0.001 PHE C 16 TYR 0.011 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 : 0.357 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9197 (mmm) cc_final: 0.8867 (mmm) REVERT: B 64 MET cc_start: 0.9385 (mmp) cc_final: 0.8984 (mmp) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.1273 time to fit residues: 2.4334 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 : 0.361 ------------------------------------------------------------------------------- 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 28 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.030109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.027037 restraints weight = 57745.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.027643 restraints weight = 33319.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.028055 restraints weight = 22214.994| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2488 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 : 0.645 10.898 4662 Z= 0.335 Chirality : 0.040 0.228 525 Planarity : 0.005 0.041 585 Dihedral : 4.611 22.258 447 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.82 % Allowed : 13.66 % Favored : 85.52 % 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: 2.62 (0.44), residues: 402 helix: 1.99 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.20 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 60 HIS 0.003 0.001 HIS C 45 PHE 0.009 0.001 PHE C 237 TYR 0.011 0.001 TYR A 272 ARG 0.003 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 13 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9198 (mmm) cc_final: 0.8947 (mmt) REVERT: B 64 MET cc_start: 0.9419 (mmp) cc_final: 0.8950 (mmt) outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.1451 time to fit residues: 2.7460 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 0.0020 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.030160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.027125 restraints weight = 57331.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.027669 restraints weight = 34917.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.028048 restraints weight = 24309.780| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3411 Z= 0.157 Angle : 0.636 10.571 4662 Z= 0.327 Chirality : 0.039 0.205 525 Planarity : 0.004 0.042 585 Dihedral : 4.425 21.405 447 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.27 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: 2.75 (0.44), residues: 402 helix: 2.06 (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 0.015 0.001 TRP C 60 HIS 0.002 0.001 HIS A 244 PHE 0.008 0.001 PHE C 16 TYR 0.010 0.001 TYR B 228 ARG 0.002 0.000 ARG B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.46 seconds wall clock time: 21 minutes 6.17 seconds (1266.17 seconds total)