Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:32:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/12_2022/7rtv_24690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/12_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_24690/12_2022/7rtv_24690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/12_2022/7rtv_24690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/12_2022/7rtv_24690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtv_24690/12_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-4807/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: 2.19, per 1000 atoms: 0.76 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: 1.67 Conformation dependent library (CDL) restraints added in 485.6 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: 0.09 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: 0.80 Time building geometry restraints manager: 1.49 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: 0.180 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: 1.250 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- 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 : 0.252 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1173 time to fit residues: 13.4547 Evaluate side-chains 75 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4395 ------------------------------------------------------------------------------- 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: 0.6365 moved from start: 0.1316 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= 0.216 Angle : 0.699 8.899 3989 Z= 0.342 Chirality : 0.042 0.245 502 Planarity : 0.004 0.047 486 Dihedral : 14.252 105.858 433 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.69 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 : 0.278 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1005 time to fit residues: 11.9612 Evaluate side-chains 83 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0297 time to fit residues: 0.6048 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.6382 moved from start: 0.1547 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= 0.215 Angle : 0.662 9.358 3989 Z= 0.323 Chirality : 0.040 0.190 502 Planarity : 0.004 0.036 486 Dihedral : 14.263 105.841 433 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 3.60 (0.43), residues: 362 helix: 2.83 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.88 (1.11), residues: 40 *********************** 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: 6 poor density : 88 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.1033 time to fit residues: 11.7113 Evaluate side-chains 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0302 time to fit residues: 0.5488 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 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 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.1784 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= 0.213 Angle : 0.723 10.171 3989 Z= 0.345 Chirality : 0.045 0.316 502 Planarity : 0.004 0.028 486 Dihedral : 14.273 105.777 433 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.65 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: 3.35 (0.43), residues: 362 helix: 2.69 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.02 (1.09), 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: 10 poor density : 97 time to evaluate : 0.274 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1015 time to fit residues: 13.0185 Evaluate side-chains 87 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0344 time to fit residues: 0.7900 ------------------------------------------------------------------------------- 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: 0.0070 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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: 0.6368 moved from start: 0.2037 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 : 0.745 10.471 3989 Z= 0.352 Chirality : 0.044 0.295 502 Planarity : 0.003 0.028 486 Dihedral : 14.265 105.477 433 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.65 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: 3.53 (0.44), residues: 362 helix: 2.81 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.94 (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: 4 poor density : 93 time to evaluate : 0.279 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 95 average time/residue: 0.1078 time to fit residues: 12.9781 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4583 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.6388 moved from start: 0.2184 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= 0.219 Angle : 0.766 11.213 3989 Z= 0.356 Chirality : 0.044 0.305 502 Planarity : 0.004 0.028 486 Dihedral : 14.282 105.816 433 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.52 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: 3.37 (0.44), residues: 362 helix: 2.70 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.95 (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 94 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.320 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.1051 time to fit residues: 11.8881 Evaluate side-chains 88 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0309 time to fit residues: 0.6478 ------------------------------------------------------------------------------- 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: 0.0270 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.6354 moved from start: 0.2247 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 : 0.793 11.245 3989 Z= 0.364 Chirality : 0.042 0.296 502 Planarity : 0.003 0.028 486 Dihedral : 14.271 105.493 433 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.00 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: 3.39 (0.44), residues: 362 helix: 2.70 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.91 (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: 3 poor density : 86 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.0996 time to fit residues: 11.1440 Evaluate side-chains 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0283 time to fit residues: 0.4543 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.6399 moved from start: 0.2361 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= 0.238 Angle : 0.807 13.229 3989 Z= 0.377 Chirality : 0.045 0.315 502 Planarity : 0.004 0.028 486 Dihedral : 14.295 105.908 433 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.21 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: 3.22 (0.44), residues: 362 helix: 2.59 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.94 (1.10), 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 90 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.274 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.1149 time to fit residues: 12.4785 Evaluate side-chains 84 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0297 time to fit residues: 0.4914 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 2932 Z= 0.235 Angle : 0.842 13.501 3989 Z= 0.388 Chirality : 0.043 0.297 502 Planarity : 0.004 0.027 486 Dihedral : 14.292 105.674 433 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 3.24 (0.44), residues: 362 helix: 2.60 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.90 (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 : 0.309 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.1053 time to fit residues: 11.9925 Evaluate side-chains 85 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0311 time to fit residues: 0.5905 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.6381 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 2932 Z= 0.253 Angle : 0.867 13.809 3989 Z= 0.407 Chirality : 0.044 0.297 502 Planarity : 0.004 0.027 486 Dihedral : 14.343 105.793 433 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.46 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: 3.01 (0.44), residues: 362 helix: 2.46 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.96 (1.07), residues: 42 ********************** 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 85 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.308 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1135 time to fit residues: 12.1495 Evaluate side-chains 82 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0293 time to fit residues: 0.4627 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4690 r_free = 0.4690 target = 0.232781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.199622 restraints weight = 4449.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.205558 restraints weight = 2824.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.209505 restraints weight = 1976.058| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 2932 Z= 0.237 Angle : 0.868 14.432 3989 Z= 0.403 Chirality : 0.043 0.278 502 Planarity : 0.004 0.027 486 Dihedral : 14.348 105.588 433 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 3.10 (0.44), residues: 362 helix: 2.51 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.82 (1.09), residues: 42 =============================================================================== Job complete usr+sys time: 872.70 seconds wall clock time: 16 minutes 39.00 seconds (999.00 seconds total)