Starting phenix.real_space_refine (version: dev) on Fri Feb 17 00:42:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/02_2023/7rtv_24690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/02_2023/7rtv_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_24690/02_2023/7rtv_24690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/02_2023/7rtv_24690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/02_2023/7rtv_24690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/02_2023/7rtv_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 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-4877/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: 2.11, per 1000 atoms: 0.73 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: 1.32 Conformation dependent library (CDL) restraints added in 428.7 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: 0.82 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 0.230 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: 1.400 Check model and map are aligned: 0.040 Process input model: 13.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- 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 : 0.296 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1318 time to fit residues: 15.1218 Evaluate side-chains 75 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4497 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6780 ------------------------------------------------------------------------------- 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: 0.6361 moved from start: 0.1320 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= 0.215 Angle : 0.702 8.960 3989 Z= 0.343 Chirality : 0.043 0.247 502 Planarity : 0.004 0.047 486 Dihedral : 14.251 105.851 433 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.00 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 101 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.351 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1143 time to fit residues: 13.4766 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0343 time to fit residues: 0.6814 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6386 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 2932 Z= 0.219 Angle : 0.672 9.382 3989 Z= 0.326 Chirality : 0.040 0.216 502 Planarity : 0.004 0.036 486 Dihedral : 14.267 105.886 433 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.13 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: 3.46 (0.43), residues: 362 helix: 2.76 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.98 (1.09), 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 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 89 average time/residue: 0.1230 time to fit residues: 13.9745 Evaluate side-chains 85 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0437 time to fit residues: 0.6627 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6390 moved from start: 0.1797 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 : 0.724 10.249 3989 Z= 0.345 Chirality : 0.044 0.308 502 Planarity : 0.004 0.028 486 Dihedral : 14.278 105.819 433 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.44), residues: 362 helix: 2.68 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.05 (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 106 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.337 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.1110 time to fit residues: 13.9186 Evaluate side-chains 87 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0338 time to fit residues: 0.7175 ------------------------------------------------------------------------------- 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: 0.0770 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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: 0.6370 moved from start: 0.1992 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= 0.209 Angle : 0.740 10.456 3989 Z= 0.347 Chirality : 0.044 0.300 502 Planarity : 0.004 0.028 486 Dihedral : 14.263 105.526 433 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.95 % 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: 3.53 (0.44), residues: 362 helix: 2.80 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.93 (1.10), 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 97 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.293 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.1121 time to fit residues: 13.1096 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0308 time to fit residues: 0.5420 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6390 moved from start: 0.2193 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= 0.230 Angle : 0.787 11.414 3989 Z= 0.366 Chirality : 0.045 0.306 502 Planarity : 0.004 0.028 486 Dihedral : 14.295 105.889 433 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.90 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: 3.36 (0.44), residues: 362 helix: 2.68 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.92 (1.11), 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 96 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.326 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 0.1146 time to fit residues: 12.8294 Evaluate side-chains 87 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0325 time to fit residues: 0.6660 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 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 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2267 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= 0.217 Angle : 0.779 12.506 3989 Z= 0.362 Chirality : 0.042 0.290 502 Planarity : 0.004 0.027 486 Dihedral : 14.291 105.700 433 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.65 % 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: 3.29 (0.44), residues: 362 helix: 2.63 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.90 (1.11), 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 89 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.330 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.1301 time to fit residues: 14.2016 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0338 time to fit residues: 0.4963 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.0070 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2406 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= 0.213 Angle : 0.811 12.379 3989 Z= 0.373 Chirality : 0.042 0.291 502 Planarity : 0.003 0.027 486 Dihedral : 14.261 105.279 433 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 3.35 (0.44), residues: 362 helix: 2.68 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.89 (1.11), 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 93 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.299 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1100 time to fit residues: 12.7517 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.4489 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 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 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 2932 Z= 0.239 Angle : 0.848 12.758 3989 Z= 0.395 Chirality : 0.048 0.340 502 Planarity : 0.004 0.028 486 Dihedral : 14.277 105.521 433 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 3.21 (0.44), residues: 362 helix: 2.58 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.93 (1.10), 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 89 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.336 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.1119 time to fit residues: 12.5109 Evaluate side-chains 89 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0334 time to fit residues: 0.6256 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 2932 Z= 0.239 Angle : 0.880 13.036 3989 Z= 0.411 Chirality : 0.047 0.301 502 Planarity : 0.004 0.027 486 Dihedral : 14.315 105.430 433 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.65 % 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: 3.04 (0.44), residues: 362 helix: 2.45 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.82 (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 93 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.1421 time to fit residues: 15.6697 Evaluate side-chains 85 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.5545 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.229719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.195660 restraints weight = 4460.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.201836 restraints weight = 2868.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.205916 restraints weight = 2036.187| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 2932 Z= 0.248 Angle : 0.876 12.419 3989 Z= 0.411 Chirality : 0.044 0.279 502 Planarity : 0.004 0.027 486 Dihedral : 14.329 105.896 433 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 2.97 (0.44), residues: 362 helix: 2.42 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.86 (1.09), residues: 42 =============================================================================== Job complete usr+sys time: 893.96 seconds wall clock time: 16 minutes 59.78 seconds (1019.78 seconds total)