Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:23:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/11_2022/7x84_33055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/11_2022/7x84_33055.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/7x84_33055/11_2022/7x84_33055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/11_2022/7x84_33055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/11_2022/7x84_33055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x84_33055/11_2022/7x84_33055.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= 0.001 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 "B ARG 180": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.22, per 1000 atoms: 0.68 Number of scatterers: 3258 At special positions: 0 Unit cell: (99.6, 107.07, 33.2, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 478.0 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.992A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.438A pdb=" N GLN B 138 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN A 138 " --> pdb=" O LYS C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 168 removed outlier: 6.865A pdb=" N ALA B 167 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 168 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 167 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN C 168 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.377A pdb=" N ILE B 176 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 176 " --> pdb=" O GLY C 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 180 through 186 removed outlier: 6.429A pdb=" N LEU B 181 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASN B 183 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ILE A 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 181 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN A 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N ILE C 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N THR A 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.664A pdb=" N TYR B 197 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR A 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 221 removed outlier: 6.645A pdb=" N THR B 215 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER A 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 217 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LYS A 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE B 219 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR A 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LYS C 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE A 219 " --> pdb=" O LYS C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.452A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY A 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE B 237 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY C 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 32 hydrogen bonds defined for protein. 96 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: 0.73 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1026 1.34 - 1.45: 518 1.45 - 1.57: 1732 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA THR C 234 " pdb=" CB THR C 234 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.35e-02 5.49e+03 3.76e+00 bond pdb=" CA THR B 234 " pdb=" CB THR B 234 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.35e-02 5.49e+03 3.40e+00 bond pdb=" CA THR A 234 " pdb=" CB THR A 234 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.35e-02 5.49e+03 3.21e+00 bond pdb=" CG1 ILE B 146 " pdb=" CD1 ILE B 146 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CG1 ILE A 146 " pdb=" CD1 ILE A 146 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.30e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 99.43 - 105.78: 35 105.78 - 112.13: 1687 112.13 - 118.48: 934 118.48 - 124.83: 1826 124.83 - 131.18: 21 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N THR C 234 " pdb=" CA THR C 234 " pdb=" C THR C 234 " ideal model delta sigma weight residual 107.23 117.63 -10.40 1.67e+00 3.59e-01 3.87e+01 angle pdb=" N THR A 234 " pdb=" CA THR A 234 " pdb=" C THR A 234 " ideal model delta sigma weight residual 107.23 117.58 -10.35 1.67e+00 3.59e-01 3.84e+01 angle pdb=" N THR B 234 " pdb=" CA THR B 234 " pdb=" C THR B 234 " ideal model delta sigma weight residual 107.23 117.57 -10.34 1.67e+00 3.59e-01 3.83e+01 angle pdb=" C THR A 234 " pdb=" CA THR A 234 " pdb=" CB THR A 234 " ideal model delta sigma weight residual 111.42 106.84 4.58 1.31e+00 5.83e-01 1.22e+01 angle pdb=" C THR C 234 " pdb=" CA THR C 234 " pdb=" CB THR C 234 " ideal model delta sigma weight residual 111.42 106.84 4.58 1.31e+00 5.83e-01 1.22e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1767 15.39 - 30.77: 157 30.77 - 46.16: 65 46.16 - 61.54: 3 61.54 - 76.93: 3 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA TYR C 135 " pdb=" C TYR C 135 " pdb=" N ASP C 136 " pdb=" CA ASP C 136 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR B 135 " pdb=" C TYR B 135 " pdb=" N ASP B 136 " pdb=" CA ASP B 136 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR A 135 " pdb=" C TYR A 135 " pdb=" N ASP A 136 " pdb=" CA ASP A 136 " ideal model delta harmonic sigma weight residual 180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 259 0.031 - 0.063: 146 0.063 - 0.094: 61 0.094 - 0.125: 62 0.125 - 0.156: 15 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB THR C 153 " pdb=" CA THR C 153 " pdb=" OG1 THR C 153 " pdb=" CG2 THR C 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 153 " pdb=" CA THR A 153 " pdb=" OG1 THR A 153 " pdb=" CG2 THR A 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB THR B 153 " pdb=" CA THR B 153 " pdb=" OG1 THR B 153 " pdb=" CG2 THR B 153 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.022 2.00e-02 2.50e+03 1.93e-02 7.43e+00 pdb=" CG TYR C 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.022 2.00e-02 2.50e+03 1.92e-02 7.34e+00 pdb=" CG TYR A 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.021 2.00e-02 2.50e+03 1.91e-02 7.33e+00 pdb=" CG TYR B 143 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.002 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 685 2.79 - 3.32: 2939 3.32 - 3.84: 5161 3.84 - 4.37: 5887 4.37 - 4.90: 11776 Nonbonded interactions: 26448 Sorted by model distance: nonbonded pdb=" O ASN A 148 " pdb=" OG1 THR A 149 " model vdw 2.259 2.440 nonbonded pdb=" O ASN C 148 " pdb=" OG1 THR C 149 " model vdw 2.259 2.440 nonbonded pdb=" O ASN B 148 " pdb=" OG1 THR B 149 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR C 236 " pdb=" O HIS C 239 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.263 2.440 ... (remaining 26443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 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: 3.120 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: 16.350 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 15.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 0.045 3312 Z= 0.521 Angle : 0.832 10.395 4503 Z= 0.490 Chirality : 0.056 0.156 543 Planarity : 0.003 0.020 558 Dihedral : 13.867 76.927 1206 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.26), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.20), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 1.2190 time to fit residues: 118.7591 Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN A 148 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 249 GLN C 148 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 245 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3312 Z= 0.145 Angle : 0.598 5.490 4503 Z= 0.334 Chirality : 0.052 0.138 543 Planarity : 0.002 0.019 558 Dihedral : 5.691 18.634 447 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 2.91 % 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: -4.66 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.23), residues: 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.437 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 92 average time/residue: 1.2267 time to fit residues: 115.8248 Evaluate side-chains 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 182 ASN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3312 Z= 0.292 Angle : 0.683 7.126 4503 Z= 0.375 Chirality : 0.052 0.149 543 Planarity : 0.003 0.024 558 Dihedral : 5.921 21.039 447 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 5.03 % 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: -4.23 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.403 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 84 average time/residue: 1.2809 time to fit residues: 110.2039 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1648 time to fit residues: 0.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.042 3312 Z= 0.445 Angle : 0.773 10.371 4503 Z= 0.424 Chirality : 0.053 0.155 543 Planarity : 0.003 0.029 558 Dihedral : 6.325 22.433 447 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 4.76 % 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: -4.20 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.342 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 87 average time/residue: 1.2618 time to fit residues: 112.5148 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3312 Z= 0.220 Angle : 0.673 9.239 4503 Z= 0.363 Chirality : 0.052 0.144 543 Planarity : 0.002 0.025 558 Dihedral : 5.866 21.975 447 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 5.03 % 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: -3.96 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.441 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 1.2427 time to fit residues: 112.2669 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2248 time to fit residues: 1.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 3312 Z= 0.421 Angle : 0.785 8.994 4503 Z= 0.425 Chirality : 0.054 0.176 543 Planarity : 0.003 0.026 558 Dihedral : 6.256 22.433 447 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 4.76 % 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: -3.95 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.416 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 82 average time/residue: 1.3162 time to fit residues: 110.6615 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 1.7239 time to fit residues: 4.2974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3312 Z= 0.280 Angle : 0.726 10.509 4503 Z= 0.389 Chirality : 0.053 0.187 543 Planarity : 0.003 0.025 558 Dihedral : 6.059 22.844 447 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 3.70 % 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: -3.85 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.389 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 1.2573 time to fit residues: 104.4738 Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN A 182 ASN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3312 Z= 0.207 Angle : 0.710 11.339 4503 Z= 0.373 Chirality : 0.052 0.186 543 Planarity : 0.002 0.025 558 Dihedral : 5.792 22.567 447 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 3.70 % 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: -3.72 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.413 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 1.1989 time to fit residues: 100.9325 Evaluate side-chains 73 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.1753 time to fit residues: 0.9491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3312 Z= 0.244 Angle : 0.721 10.684 4503 Z= 0.381 Chirality : 0.052 0.199 543 Planarity : 0.003 0.023 558 Dihedral : 5.830 22.735 447 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 3.44 % 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: -3.66 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.302 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 1.2552 time to fit residues: 102.8757 Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3312 Z= 0.242 Angle : 0.750 10.720 4503 Z= 0.393 Chirality : 0.052 0.192 543 Planarity : 0.003 0.025 558 Dihedral : 5.826 22.417 447 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 2.38 % 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: -3.63 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.27), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.439 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 1.2231 time to fit residues: 97.9795 Evaluate side-chains 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 229 GLN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.146012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.131730 restraints weight = 5042.284| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.91 r_work: 0.4201 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.4184 rms_B_bonded: 1.75 restraints_weight: 0.1250 r_work: 0.4175 rms_B_bonded: 1.83 restraints_weight: 0.0625 r_work: 0.4166 rms_B_bonded: 1.94 restraints_weight: 0.0312 r_work: 0.4156 rms_B_bonded: 2.09 restraints_weight: 0.0156 r_work: 0.4145 rms_B_bonded: 2.28 restraints_weight: 0.0078 r_work: 0.4133 rms_B_bonded: 2.50 restraints_weight: 0.0039 r_work: 0.4120 rms_B_bonded: 2.77 restraints_weight: 0.0020 r_work: 0.4105 rms_B_bonded: 3.08 restraints_weight: 0.0010 r_work: 0.4089 rms_B_bonded: 3.45 restraints_weight: 0.0005 r_work: 0.4071 rms_B_bonded: 3.87 restraints_weight: 0.0002 r_work: 0.4051 rms_B_bonded: 4.37 restraints_weight: 0.0001 r_work: 0.4030 rms_B_bonded: 4.96 restraints_weight: 0.0001 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3312 Z= 0.222 Angle : 0.770 12.887 4503 Z= 0.389 Chirality : 0.052 0.144 543 Planarity : 0.003 0.026 558 Dihedral : 5.792 22.431 447 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.27), residues: 399 =============================================================================== Job complete usr+sys time: 2191.79 seconds wall clock time: 39 minutes 57.90 seconds (2397.90 seconds total)