Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 12:47:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/08_2023/8ber_16009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/08_2023/8ber_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_16009/08_2023/8ber_16009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/08_2023/8ber_16009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/08_2023/8ber_16009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ber_16009/08_2023/8ber_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 2.18, per 1000 atoms: 0.66 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: 1.41 Conformation dependent library (CDL) restraints added in 474.2 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: 0.25 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: 0.79 Time building geometry restraints manager: 1.50 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: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.530 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1537 time to fit residues: 4.2899 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5516 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 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: 0.7980 moved from start: 0.0811 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= 0.234 Angle : 0.628 7.403 4662 Z= 0.335 Chirality : 0.042 0.284 525 Planarity : 0.005 0.040 585 Dihedral : 4.632 21.999 447 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.44), residues: 402 helix: 1.99 (0.31), residues: 297 sheet: None (None), residues: 0 loop : 1.14 (0.67), residues: 105 *********************** 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 : 0.372 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.1324 time to fit residues: 2.7021 Evaluate side-chains 13 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0370 time to fit residues: 0.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 50.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3411 Z= 0.237 Angle : 0.625 8.681 4662 Z= 0.323 Chirality : 0.040 0.268 525 Planarity : 0.004 0.045 585 Dihedral : 4.661 22.590 447 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.44), residues: 402 helix: 1.95 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.18 (0.67), residues: 103 *********************** 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 : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.1425 time to fit residues: 3.1977 Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0616 time to fit residues: 0.6984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 16 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 50.0000 chunk 10 optimal weight: 0.0370 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 10.8070 ------------------------------------------------------------------------------- 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: 0.8004 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 3411 Z= 0.318 Angle : 0.681 9.895 4662 Z= 0.347 Chirality : 0.041 0.281 525 Planarity : 0.005 0.044 585 Dihedral : 4.821 23.905 447 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.44), residues: 402 helix: 1.97 (0.31), residues: 297 sheet: None (None), residues: 0 loop : 1.13 (0.66), residues: 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.1387 time to fit residues: 2.9403 Evaluate side-chains 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 10 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0480 time to fit residues: 0.6728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.1599 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= 0.180 Angle : 0.615 10.879 4662 Z= 0.305 Chirality : 0.039 0.235 525 Planarity : 0.004 0.043 585 Dihedral : 4.713 23.277 447 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 1.09 % 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: 2.73 (0.44), residues: 402 helix: 2.07 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.26 (0.68), residues: 103 *********************** 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 : 0.425 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 16 average time/residue: 0.1348 time to fit residues: 3.2118 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 27 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: 0.7979 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3411 Z= 0.198 Angle : 0.630 12.158 4662 Z= 0.314 Chirality : 0.039 0.226 525 Planarity : 0.004 0.041 585 Dihedral : 4.627 22.935 447 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.44), residues: 402 helix: 2.07 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.40 (0.68), residues: 103 *********************** 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 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.417 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.1249 time to fit residues: 2.5140 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.8000 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3411 Z= 0.253 Angle : 0.626 12.548 4662 Z= 0.316 Chirality : 0.040 0.235 525 Planarity : 0.004 0.042 585 Dihedral : 4.661 23.166 447 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.44), residues: 402 helix: 2.10 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.34 (0.68), residues: 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 10 time to evaluate : 0.427 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.1468 time to fit residues: 2.7476 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0345 time to fit residues: 0.5983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3411 Z= 0.247 Angle : 0.685 13.343 4662 Z= 0.343 Chirality : 0.040 0.236 525 Planarity : 0.004 0.041 585 Dihedral : 4.689 23.265 447 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.00 % 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: 2.79 (0.44), residues: 402 helix: 2.09 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 1.34 (0.68), residues: 103 *********************** 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 10 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1506 time to fit residues: 2.4457 Evaluate side-chains 10 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 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: 0.7983 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3411 Z= 0.210 Angle : 0.630 12.994 4662 Z= 0.322 Chirality : 0.039 0.223 525 Planarity : 0.004 0.041 585 Dihedral : 4.624 22.886 447 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.44), residues: 402 helix: 2.10 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.40 (0.68), residues: 103 *********************** 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 12 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.411 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 0.1315 time to fit residues: 2.3632 Evaluate side-chains 10 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 0.0020 chunk 31 optimal weight: 6.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- 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: 0.7984 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3411 Z= 0.196 Angle : 0.621 12.787 4662 Z= 0.318 Chirality : 0.038 0.220 525 Planarity : 0.004 0.041 585 Dihedral : 4.500 22.212 447 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.00 % 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: 2.78 (0.45), residues: 402 helix: 2.05 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.44 (0.68), residues: 103 ********************** 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 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.376 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1392 time to fit residues: 2.4932 Evaluate side-chains 11 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.0570 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.030655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.027618 restraints weight = 56433.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.028182 restraints weight = 34737.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.028602 restraints weight = 24065.203| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3411 Z= 0.188 Angle : 0.608 12.722 4662 Z= 0.311 Chirality : 0.038 0.215 525 Planarity : 0.004 0.041 585 Dihedral : 4.435 21.649 447 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.45), residues: 402 helix: 2.15 (0.32), residues: 299 sheet: None (None), residues: 0 loop : 1.51 (0.69), residues: 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 867.91 seconds wall clock time: 16 minutes 34.61 seconds (994.61 seconds total)