Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:33:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/04_2022/7rtv_24690.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 2881 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2803 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 7, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.35, per 1000 atoms: 0.82 Number of scatterers: 2881 At special positions: 0 Unit cell: (62.863, 52.669, 135.92, 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 25 16.00 O 550 8.00 N 460 7.00 C 1846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 129 " " NAG C 1 " - " ASN A 352 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 438.4 milliseconds 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 4.152A pdb=" N CYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 240 through 274 removed outlier: 3.951A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.318A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 removed outlier: 3.507A pdb=" N LEU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.618A pdb=" N GLU A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 409 removed outlier: 4.054A pdb=" N ASP A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 280 hydrogen bonds defined for protein. 834 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: 0.75 Time building geometry restraints manager: 1.58 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: 903 1.34 - 1.46: 530 1.46 - 1.58: 1465 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2932 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.412 1.452 -0.040 3.50e-02 8.16e+02 1.28e+00 bond pdb=" CG MET A 177 " pdb=" SD MET A 177 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.12e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.538 1.574 -0.036 3.60e-02 7.72e+02 1.00e+00 bond pdb=" C1 NAG B 2 " pdb=" C2 NAG B 2 " ideal model delta sigma weight residual 1.526 1.543 -0.017 2.00e-02 2.50e+03 7.57e-01 bond pdb=" CB LEU A 350 " pdb=" CG LEU A 350 " ideal model delta sigma weight residual 1.530 1.513 0.017 2.00e-02 2.50e+03 7.26e-01 ... (remaining 2927 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 40 106.20 - 113.14: 1678 113.14 - 120.08: 1051 120.08 - 127.02: 1198 127.02 - 133.97: 22 Bond angle restraints: 3989 Sorted by residual: angle pdb=" C GLN A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.58 113.37 8.21 1.95e+00 2.63e-01 1.77e+01 angle pdb=" CA MET A 177 " pdb=" CB MET A 177 " pdb=" CG MET A 177 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.33e+00 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 121.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" N MET A 177 " pdb=" CA MET A 177 " pdb=" CB MET A 177 " ideal model delta sigma weight residual 110.41 115.33 -4.92 1.68e+00 3.54e-01 8.59e+00 angle pdb=" CA GLN A 144 " pdb=" CB GLN A 144 " pdb=" CG GLN A 144 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.37e+00 ... (remaining 3984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 1583 21.10 - 42.20: 113 42.20 - 63.30: 18 63.30 - 84.40: 6 84.40 - 105.51: 6 Dihedral angle restraints: 1726 sinusoidal: 668 harmonic: 1058 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 172.83 -79.83 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" C2 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" C4 NAG B 1 " pdb=" C5 NAG B 1 " ideal model delta sinusoidal sigma weight residual 50.00 -55.51 105.51 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C1 NAG B 2 " pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " ideal model delta sinusoidal sigma weight residual -50.00 53.54 -103.54 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 1723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 370 0.039 - 0.078: 104 0.078 - 0.117: 21 0.117 - 0.156: 4 0.156 - 0.195: 3 Chirality restraints: 502 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB ILE A 305 " pdb=" CA ILE A 305 " pdb=" CG1 ILE A 305 " pdb=" CG2 ILE A 305 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA MET A 177 " pdb=" N MET A 177 " pdb=" C MET A 177 " pdb=" CB MET A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 499 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 410 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 411 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ILE A 381 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 382 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C CYS A 382 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS A 382 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 383 " -0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 387 2.75 - 3.28: 3201 3.28 - 3.82: 5090 3.82 - 4.36: 5147 4.36 - 4.90: 8800 Nonbonded interactions: 22625 Sorted by model distance: nonbonded pdb=" O SER A 256 " pdb=" OG SER A 396 " model vdw 2.207 2.440 nonbonded pdb=" O GLY A 117 " pdb=" NE2 GLN A 120 " model vdw 2.228 2.520 nonbonded pdb=" O SER A 183 " pdb=" OG SER A 186 " model vdw 2.259 2.440 nonbonded pdb=" O CYS A 300 " pdb=" NH2 ARG A 368 " model vdw 2.308 2.520 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE2 GLU A 209 " model vdw 2.319 2.520 ... (remaining 22620 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 1846 2.51 5 N 460 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.190 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: 1.260 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 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 0.040 2932 Z= 0.206 Angle : 0.682 8.808 3989 Z= 0.336 Chirality : 0.040 0.195 502 Planarity : 0.005 0.080 486 Dihedral : 16.494 105.506 1040 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.32 % 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: 3.61 (0.44), residues: 362 helix: 2.84 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.76 (1.14), residues: 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.289 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1245 time to fit residues: 14.3948 Evaluate side-chains 75 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 152 GLN A 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 2932 Z= 0.210 Angle : 0.699 8.933 3989 Z= 0.342 Chirality : 0.042 0.236 502 Planarity : 0.004 0.041 486 Dihedral : 14.252 105.864 433 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 2.60 % 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: 3.61 (0.43), residues: 362 helix: 2.85 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.94 (1.09), residues: 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.239 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.0915 time to fit residues: 10.8472 Evaluate side-chains 85 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0270 time to fit residues: 0.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 2932 Z= 0.220 Angle : 0.692 9.412 3989 Z= 0.332 Chirality : 0.041 0.230 502 Planarity : 0.004 0.032 486 Dihedral : 14.268 105.907 433 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.62 % 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: 3.39 (0.43), residues: 362 helix: 2.72 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.06 (1.07), residues: 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.1089 time to fit residues: 12.7107 Evaluate side-chains 87 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0307 time to fit residues: 0.5898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.0050 chunk 19 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 2932 Z= 0.217 Angle : 0.746 10.323 3989 Z= 0.351 Chirality : 0.045 0.311 502 Planarity : 0.004 0.028 486 Dihedral : 14.268 105.617 433 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 3.57 % 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: 3.35 (0.43), residues: 362 helix: 2.69 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.06 (1.08), residues: 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.314 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.1090 time to fit residues: 13.8672 Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0360 time to fit residues: 0.7912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 2932 Z= 0.319 Angle : 0.782 10.897 3989 Z= 0.388 Chirality : 0.045 0.279 502 Planarity : 0.004 0.029 486 Dihedral : 14.404 107.368 433 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.60 % 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: 2.98 (0.43), residues: 362 helix: 2.42 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.92 (1.09), residues: 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.337 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1075 time to fit residues: 12.7914 Evaluate side-chains 91 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0307 time to fit residues: 0.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 2932 Z= 0.221 Angle : 0.752 10.212 3989 Z= 0.358 Chirality : 0.046 0.295 502 Planarity : 0.004 0.027 486 Dihedral : 14.356 106.069 433 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.43), residues: 362 helix: 2.48 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.94 (1.09), residues: 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.313 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 0.1062 time to fit residues: 12.1189 Evaluate side-chains 87 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0316 time to fit residues: 0.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 0.040 2932 Z= 0.209 Angle : 0.785 11.885 3989 Z= 0.363 Chirality : 0.042 0.291 502 Planarity : 0.004 0.028 486 Dihedral : 14.324 105.489 433 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.97 % 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: 3.10 (0.44), residues: 362 helix: 2.50 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.85 (1.14), residues: 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.309 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1072 time to fit residues: 12.4364 Evaluate side-chains 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0321 time to fit residues: 0.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 2932 Z= 0.216 Angle : 0.823 12.294 3989 Z= 0.383 Chirality : 0.045 0.302 502 Planarity : 0.004 0.028 486 Dihedral : 14.312 105.378 433 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.62 % 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: 2.93 (0.43), residues: 362 helix: 2.39 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.89 (1.13), residues: 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.326 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.1141 time to fit residues: 13.2896 Evaluate side-chains 91 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0318 time to fit residues: 0.6560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS A 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 2932 Z= 0.227 Angle : 0.879 12.558 3989 Z= 0.412 Chirality : 0.047 0.299 502 Planarity : 0.004 0.027 486 Dihedral : 14.335 105.132 433 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 2.83 (0.44), residues: 362 helix: 2.32 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.90 (1.13), residues: 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1039 time to fit residues: 11.3069 Evaluate side-chains 82 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 2932 Z= 0.246 Angle : 0.870 13.101 3989 Z= 0.413 Chirality : 0.047 0.306 502 Planarity : 0.004 0.028 486 Dihedral : 14.362 105.378 433 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.44), residues: 362 helix: 2.13 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.93 (1.11), residues: 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.322 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.1101 time to fit residues: 11.7860 Evaluate side-chains 89 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0327 time to fit residues: 0.6000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.231515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.197830 restraints weight = 4564.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.203997 restraints weight = 2940.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.208222 restraints weight = 2076.319| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 2932 Z= 0.233 Angle : 0.866 13.431 3989 Z= 0.408 Chirality : 0.045 0.285 502 Planarity : 0.004 0.027 486 Dihedral : 14.343 105.390 433 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 2.57 (0.44), residues: 362 helix: 2.16 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.99 (1.09), residues: 42 =============================================================================== Job complete usr+sys time: 861.50 seconds wall clock time: 16 minutes 16.04 seconds (976.04 seconds total)