Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:41:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voj_32050/02_2023/7voj_32050_updated.pdb" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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 ARG 5": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6318 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.14, per 1000 atoms: 0.66 Number of scatterers: 6318 At special positions: 0 Unit cell: (84.162, 84.162, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 Al 2 13.00 O 1158 8.00 N 1052 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.845A pdb=" N VAL A 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 36 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 41 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 106 through 126 removed outlier: 4.314A pdb=" N PHE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 157 through 182 Processing helix chain 'A' and resid 188 through 215 removed outlier: 5.818A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.754A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.397A pdb=" N TRP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 293 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 307 through 330 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.658A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 398 Processing helix chain 'B' and resid 2 through 17 Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.845A pdb=" N VAL B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 36 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 106 through 126 removed outlier: 4.314A pdb=" N PHE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 135 through 149 Processing helix chain 'B' and resid 157 through 182 Processing helix chain 'B' and resid 188 through 215 removed outlier: 5.818A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 removed outlier: 4.754A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 4.397A pdb=" N TRP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 293 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 330 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.658A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 398 482 hydrogen bonds defined for protein. 1356 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: 1.94 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1610 1.33 - 1.45: 1186 1.45 - 1.57: 3588 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6440 Sorted by residual: bond pdb=" C CYS A 184 " pdb=" O CYS A 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C CYS B 184 " pdb=" O CYS B 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C GLY A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" C GLY B 102 " pdb=" N ALA B 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.37e-02 5.33e+03 3.59e+00 ... (remaining 6435 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.48: 150 106.48 - 113.37: 3558 113.37 - 120.26: 2666 120.26 - 127.15: 2272 127.15 - 134.04: 52 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" C PHE B 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE B 182 " pdb=" CA PHE B 182 " pdb=" C PHE B 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N PHE A 182 " pdb=" CA PHE A 182 " pdb=" C PHE A 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 110.62 117.44 -6.82 1.02e+00 9.61e-01 4.48e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 3354 14.31 - 28.62: 372 28.62 - 42.93: 88 42.93 - 57.24: 30 57.24 - 71.55: 6 Dihedral angle restraints: 3850 sinusoidal: 1526 harmonic: 2324 Sorted by residual: dihedral pdb=" CA ARG B 154 " pdb=" C ARG B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 154 " pdb=" C ARG A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 866 0.081 - 0.162: 110 0.162 - 0.243: 14 0.243 - 0.324: 2 0.324 - 0.404: 4 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PHE B 182 " pdb=" N PHE B 182 " pdb=" C PHE B 182 " pdb=" CB PHE B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 182 " pdb=" N PHE A 182 " pdb=" C PHE A 182 " pdb=" CB PHE A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 51 " pdb=" N PHE A 51 " pdb=" C PHE A 51 " pdb=" CB PHE A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 993 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 180 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER B 180 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 181 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 180 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 180 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 181 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 185 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.042 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 96 2.63 - 3.20: 5512 3.20 - 3.76: 9632 3.76 - 4.33: 12838 4.33 - 4.90: 21621 Nonbonded interactions: 49699 Sorted by model distance: nonbonded pdb=" OD1 ASP A 160 " pdb="AL AL A 603 " model vdw 2.061 2.020 nonbonded pdb=" OD1 ASP B 160 " pdb="AL AL B 603 " model vdw 2.061 2.020 nonbonded pdb=" OD2 ASP B 160 " pdb="AL AL B 603 " model vdw 2.113 2.020 nonbonded pdb=" OD2 ASP A 160 " pdb="AL AL A 603 " model vdw 2.113 2.020 nonbonded pdb=" O ACY B 601 " pdb="AL AL B 603 " model vdw 2.116 2.020 ... (remaining 49694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5 Type Number sf(0) Gaussians Al 2 5.89 5 S 32 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1158 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 individual isotropic 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 2.100 Check model and map are aligned: 0.090 Process input model: 20.230 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.008 0.057 6440 Z= 0.528 Angle : 1.008 10.902 8698 Z= 0.626 Chirality : 0.062 0.404 996 Planarity : 0.007 0.071 1094 Dihedral : 13.588 71.548 2346 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer Outliers : 1.73 % 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: -2.46 (0.26), residues: 792 helix: -1.27 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.60), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.740 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 149 average time/residue: 1.0506 time to fit residues: 165.2892 Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0585 time to fit residues: 1.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 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 289 ASN A 293 ASN A 330 GLN A 403 ASN B 289 ASN B 293 ASN B 330 GLN B 403 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 6440 Z= 0.155 Angle : 0.496 5.687 8698 Z= 0.271 Chirality : 0.035 0.147 996 Planarity : 0.004 0.042 1094 Dihedral : 4.386 17.677 858 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 4.18 % 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: 0.85 (0.30), residues: 792 helix: 1.23 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.70 (0.51), residues: 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.813 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 131 average time/residue: 0.9596 time to fit residues: 133.8274 Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.0483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 293 ASN B 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 6440 Z= 0.163 Angle : 0.472 5.554 8698 Z= 0.252 Chirality : 0.035 0.146 996 Planarity : 0.004 0.043 1094 Dihedral : 3.997 17.302 858 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 5.04 % 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: 1.88 (0.31), residues: 792 helix: 2.07 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -2.72 (0.48), residues: 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 0.791 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 123 average time/residue: 0.9156 time to fit residues: 120.7688 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 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 266 HIS ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 6440 Z= 0.147 Angle : 0.451 5.692 8698 Z= 0.241 Chirality : 0.034 0.146 996 Planarity : 0.003 0.040 1094 Dihedral : 3.839 17.490 858 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 4.18 % 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: 2.33 (0.31), residues: 792 helix: 2.39 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -2.64 (0.48), residues: 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.709 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 126 average time/residue: 0.8119 time to fit residues: 109.9825 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 1 average time/residue: 0.1060 time to fit residues: 1.2637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 6440 Z= 0.142 Angle : 0.456 7.053 8698 Z= 0.237 Chirality : 0.034 0.141 996 Planarity : 0.003 0.039 1094 Dihedral : 3.733 16.996 858 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.31), residues: 792 helix: 2.59 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -2.50 (0.49), residues: 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.770 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 114 average time/residue: 0.8109 time to fit residues: 99.5053 Evaluate side-chains 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 4 average time/residue: 0.5884 time to fit residues: 3.6256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6440 Z= 0.165 Angle : 0.468 6.834 8698 Z= 0.244 Chirality : 0.035 0.129 996 Planarity : 0.003 0.035 1094 Dihedral : 3.752 17.486 858 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 4.32 % 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: 2.70 (0.31), residues: 792 helix: 2.66 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.66 (0.48), residues: 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 0.805 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 114 average time/residue: 0.8692 time to fit residues: 106.2534 Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.1143 time to fit residues: 1.2923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 6440 Z= 0.146 Angle : 0.455 7.107 8698 Z= 0.236 Chirality : 0.034 0.128 996 Planarity : 0.003 0.034 1094 Dihedral : 3.682 17.678 858 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.31), residues: 792 helix: 2.79 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.64 (0.49), residues: 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.762 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.8414 time to fit residues: 103.8077 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6440 Z= 0.219 Angle : 0.479 6.392 8698 Z= 0.254 Chirality : 0.036 0.132 996 Planarity : 0.003 0.038 1094 Dihedral : 3.806 18.313 858 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.31), residues: 792 helix: 2.70 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -2.69 (0.48), residues: 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.788 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 0.8830 time to fit residues: 107.1739 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.2595 time to fit residues: 1.6701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 6440 Z= 0.298 Angle : 0.538 6.591 8698 Z= 0.283 Chirality : 0.038 0.137 996 Planarity : 0.004 0.035 1094 Dihedral : 3.999 19.213 858 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 4.18 % 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: 2.45 (0.31), residues: 792 helix: 2.45 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.65 (0.50), residues: 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.768 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 117 average time/residue: 0.8385 time to fit residues: 105.3647 Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 4 average time/residue: 0.0829 time to fit residues: 1.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 6440 Z= 0.164 Angle : 0.481 7.756 8698 Z= 0.252 Chirality : 0.035 0.131 996 Planarity : 0.003 0.032 1094 Dihedral : 3.769 18.907 858 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.31), residues: 792 helix: 2.71 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -2.67 (0.49), residues: 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.768 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.8527 time to fit residues: 100.3140 Evaluate side-chains 102 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.0060 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 340 HIS B 266 HIS B 340 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112027 restraints weight = 7255.432| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.10 r_work: 0.3102 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 6440 Z= 0.134 Angle : 0.468 7.347 8698 Z= 0.240 Chirality : 0.034 0.126 996 Planarity : 0.003 0.033 1094 Dihedral : 3.591 17.835 858 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.16 % 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 (0.31), residues: 792 helix: 2.91 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.49 (0.50), residues: 140 =============================================================================== Job complete usr+sys time: 2397.32 seconds wall clock time: 43 minutes 42.59 seconds (2622.59 seconds total)