Starting phenix.real_space_refine on Sun Mar 10 16:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_16009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_16009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_16009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_16009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/03_2024/8ber_16009.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.30, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 1.31 Conformation dependent library (CDL) restraints added in 593.6 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: 0.80 Time building geometry restraints manager: 1.41 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: 97.05 - 104.44: 80 104.44 - 111.83: 1682 111.83 - 119.22: 1095 119.22 - 126.61: 1716 126.61 - 134.00: 89 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 2.520 nonbonded pdb=" O VAL A 11 " pdb=" OG SER A 15 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASN C 230 " pdb=" N THR C 231 " model vdw 2.241 2.520 nonbonded pdb=" OE2 GLU A 6 " pdb=" NH1 ARG B 54 " model vdw 2.256 2.520 nonbonded pdb=" O VAL A 229 " pdb=" N GLY A 234 " model vdw 2.284 2.520 ... (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 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.650 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.660 Find NCS groups from input model: 0.190 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.389 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: 0.1393 time to fit residues: 3.8951 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0817 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= 0.230 Angle : 0.598 6.941 4662 Z= 0.323 Chirality : 0.041 0.283 525 Planarity : 0.005 0.041 585 Dihedral : 4.580 22.011 447 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.27 % Allowed : 7.10 % Favored : 92.62 % 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: 2.66 (0.44), residues: 402 helix: 2.04 (0.31), residues: 297 sheet: None (None), residues: 0 loop : 1.17 (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 0.018 0.001 PHE B 237 TYR 0.007 0.001 TYR C 272 ARG 0.005 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 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.419 Fit side-chains REVERT: A 64 MET cc_start: 0.9429 (mmp) cc_final: 0.9181 (mmt) REVERT: A 233 MET cc_start: 0.9438 (mpp) cc_final: 0.9073 (mpp) REVERT: B 64 MET cc_start: 0.9286 (mmp) cc_final: 0.8850 (mmt) REVERT: C 64 MET cc_start: 0.9407 (mmp) cc_final: 0.9184 (mmt) outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.1266 time to fit residues: 2.6577 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.0050 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3411 Z= 0.169 Angle : 0.535 5.688 4662 Z= 0.284 Chirality : 0.038 0.242 525 Planarity : 0.004 0.045 585 Dihedral : 4.476 22.116 447 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.82 % Allowed : 9.29 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.44), residues: 402 helix: 2.10 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.23 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.002 0.001 HIS B 45 PHE 0.009 0.001 PHE C 16 TYR 0.010 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 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9435 (mmp) cc_final: 0.9184 (mmt) REVERT: A 233 MET cc_start: 0.9522 (mpp) cc_final: 0.9120 (mpp) REVERT: B 64 MET cc_start: 0.9295 (mmp) cc_final: 0.8900 (mmt) REVERT: C 64 MET cc_start: 0.9396 (mmp) cc_final: 0.9114 (mmt) REVERT: C 253 GLU cc_start: 0.9651 (pm20) cc_final: 0.9389 (pm20) outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.1363 time to fit residues: 3.0548 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN 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 18 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 0 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: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3411 Z= 0.233 Angle : 0.561 7.496 4662 Z= 0.301 Chirality : 0.038 0.238 525 Planarity : 0.004 0.043 585 Dihedral : 4.487 22.566 447 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.09 % Allowed : 11.48 % Favored : 87.43 % 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: 2.87 (0.44), residues: 402 helix: 2.18 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.27 (0.68), 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 0.008 0.001 PHE A 21 TYR 0.010 0.001 TYR B 228 ARG 0.004 0.000 ARG A 252 *********************** 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 16 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9442 (mmp) cc_final: 0.9182 (mmt) REVERT: B 64 MET cc_start: 0.9309 (mmp) cc_final: 0.8919 (mmt) REVERT: C 64 MET cc_start: 0.9388 (mmp) cc_final: 0.9110 (mmt) outliers start: 4 outliers final: 3 residues processed: 15 average time/residue: 0.1403 time to fit residues: 3.1419 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 0.0060 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 overall best weight: 2.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3411 Z= 0.149 Angle : 0.521 6.919 4662 Z= 0.275 Chirality : 0.036 0.196 525 Planarity : 0.004 0.041 585 Dihedral : 4.333 21.729 447 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.09 % Allowed : 11.48 % Favored : 87.43 % 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: 2.95 (0.44), residues: 402 helix: 2.23 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.30 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 265 HIS 0.002 0.001 HIS A 244 PHE 0.008 0.001 PHE C 16 TYR 0.009 0.001 TYR B 228 ARG 0.002 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 16 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9436 (mmp) cc_final: 0.9178 (mmt) REVERT: A 233 MET cc_start: 0.9539 (mpp) cc_final: 0.9143 (mpp) REVERT: B 64 MET cc_start: 0.9363 (mmp) cc_final: 0.8925 (mmt) REVERT: C 64 MET cc_start: 0.9403 (mmp) cc_final: 0.9136 (mmt) REVERT: C 253 GLU cc_start: 0.9630 (pm20) cc_final: 0.9358 (pm20) outliers start: 4 outliers final: 3 residues processed: 15 average time/residue: 0.1342 time to fit residues: 3.0148 Evaluate side-chains 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1617 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= 0.185 Angle : 0.543 9.099 4662 Z= 0.289 Chirality : 0.037 0.200 525 Planarity : 0.004 0.039 585 Dihedral : 4.298 21.650 447 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.82 % Allowed : 12.84 % 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: 3.03 (0.44), residues: 402 helix: 2.27 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.40 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 69 HIS 0.002 0.001 HIS B 45 PHE 0.007 0.001 PHE A 21 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG A 252 *********************** 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 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9428 (mmp) cc_final: 0.9175 (mmt) REVERT: A 233 MET cc_start: 0.9545 (mpp) cc_final: 0.9139 (mpp) REVERT: B 64 MET cc_start: 0.9361 (mmp) cc_final: 0.8892 (mmt) REVERT: C 64 MET cc_start: 0.9420 (mmp) cc_final: 0.9173 (mmt) REVERT: C 253 GLU cc_start: 0.9626 (pm20) cc_final: 0.9363 (pm20) outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.1376 time to fit residues: 2.9366 Evaluate side-chains 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3411 Z= 0.177 Angle : 0.537 9.251 4662 Z= 0.283 Chirality : 0.037 0.193 525 Planarity : 0.004 0.041 585 Dihedral : 4.235 21.678 447 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.37 % Allowed : 12.57 % Favored : 86.07 % 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: 3.08 (0.44), residues: 402 helix: 2.33 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.36 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 265 HIS 0.002 0.001 HIS C 45 PHE 0.009 0.001 PHE C 16 TYR 0.009 0.001 TYR B 228 ARG 0.001 0.000 ARG A 267 *********************** 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 17 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 12 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9433 (mmp) cc_final: 0.9187 (mmt) REVERT: A 233 MET cc_start: 0.9538 (mpp) cc_final: 0.9086 (mpp) REVERT: B 64 MET cc_start: 0.9379 (mmp) cc_final: 0.8957 (mmt) REVERT: C 64 MET cc_start: 0.9411 (mmp) cc_final: 0.9055 (mmm) REVERT: C 253 GLU cc_start: 0.9643 (pm20) cc_final: 0.9387 (pm20) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.1363 time to fit residues: 3.2030 Evaluate side-chains 16 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 257 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3411 Z= 0.229 Angle : 0.560 8.016 4662 Z= 0.298 Chirality : 0.037 0.204 525 Planarity : 0.004 0.040 585 Dihedral : 4.320 22.131 447 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 3.13 (0.45), residues: 402 helix: 2.37 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.35 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS B 45 PHE 0.008 0.001 PHE A 21 TYR 0.011 0.001 TYR A 272 ARG 0.003 0.000 ARG A 267 *********************** 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 fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9451 (mmp) cc_final: 0.9202 (mmt) REVERT: A 233 MET cc_start: 0.9544 (mpp) cc_final: 0.9090 (mpp) REVERT: B 64 MET cc_start: 0.9383 (mmp) cc_final: 0.8930 (mmt) REVERT: C 64 MET cc_start: 0.9425 (mmp) cc_final: 0.9069 (mmt) REVERT: C 253 GLU cc_start: 0.9633 (pm20) cc_final: 0.9386 (pm20) outliers start: 4 outliers final: 3 residues processed: 14 average time/residue: 0.2334 time to fit residues: 4.3441 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2122 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 : 0.539 8.553 4662 Z= 0.286 Chirality : 0.037 0.193 525 Planarity : 0.005 0.050 585 Dihedral : 4.278 22.073 447 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: 3.07 (0.44), residues: 402 helix: 2.34 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.27 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.002 0.001 HIS C 45 PHE 0.008 0.001 PHE A 7 TYR 0.009 0.001 TYR B 228 ARG 0.005 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 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9450 (mmp) cc_final: 0.9203 (mmt) REVERT: B 64 MET cc_start: 0.9408 (mmp) cc_final: 0.8969 (mmt) REVERT: C 64 MET cc_start: 0.9419 (mmp) cc_final: 0.9041 (mmt) REVERT: C 253 GLU cc_start: 0.9637 (pm20) cc_final: 0.9397 (pm20) outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.1457 time to fit residues: 3.0699 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3411 Z= 0.169 Angle : 0.534 8.462 4662 Z= 0.283 Chirality : 0.036 0.189 525 Planarity : 0.004 0.039 585 Dihedral : 4.134 21.310 447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.82 % Allowed : 14.48 % Favored : 84.70 % 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: 3.17 (0.44), residues: 402 helix: 2.38 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.42 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.002 0.001 HIS C 45 PHE 0.007 0.001 PHE C 16 TYR 0.008 0.001 TYR A 272 ARG 0.006 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 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9447 (mmp) cc_final: 0.9200 (mmt) REVERT: A 233 MET cc_start: 0.9516 (mpp) cc_final: 0.9062 (mpp) REVERT: B 64 MET cc_start: 0.9406 (mmp) cc_final: 0.8945 (mmt) REVERT: C 64 MET cc_start: 0.9417 (mmp) cc_final: 0.9095 (mmm) REVERT: C 253 GLU cc_start: 0.9642 (pm20) cc_final: 0.9399 (pm20) outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.1428 time to fit residues: 3.0057 Evaluate side-chains 15 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain C residue 257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.029947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.026931 restraints weight = 56823.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.027466 restraints weight = 35116.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.027852 restraints weight = 24423.678| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3411 Z= 0.207 Angle : 0.550 8.022 4662 Z= 0.292 Chirality : 0.037 0.203 525 Planarity : 0.005 0.042 585 Dihedral : 4.224 22.129 447 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.82 % Allowed : 14.48 % Favored : 84.70 % 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: 3.15 (0.45), residues: 402 helix: 2.39 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.35 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.003 0.001 HIS C 45 PHE 0.007 0.001 PHE C 16 TYR 0.010 0.001 TYR A 272 ARG 0.008 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 854.38 seconds wall clock time: 16 minutes 17.39 seconds (977.39 seconds total)