Starting phenix.real_space_refine (version: dev) on Mon Apr 4 14:50:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/04_2022/7u15_26278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/04_2022/7u15_26278.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/7u15_26278/04_2022/7u15_26278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/04_2022/7u15_26278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/04_2022/7u15_26278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/04_2022/7u15_26278.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= 0.001 sd= 0.006 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 132, 'PCIS': 1} Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 132, 'PCIS': 1} Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 132, 'PCIS': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.75, per 1000 atoms: 0.56 Number of scatterers: 6684 At special positions: 0 Unit cell: (93.183, 114.123, 39.786, 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 21 16.00 O 699 8.00 N 531 7.00 C 2178 6.00 H 3255 1.00 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=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 151 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 151 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 151 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 547.6 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, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.773A pdb=" N ASP B 122 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.649A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.475A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.827A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.076A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.608A pdb=" N ASN B 156 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.542A pdb=" N VAL B 169 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.623A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.467A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.381A pdb=" N ILE B 195 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.009A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.784A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.077A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 231 removed outlier: 6.833A pdb=" N THR A 231 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 235 through 236 removed outlier: 6.851A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 2.23 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3255 1.03 - 1.23: 37 1.23 - 1.42: 1399 1.42 - 1.62: 2011 1.62 - 1.81: 36 Bond restraints: 6738 Sorted by residual: bond pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.18e+00 bond pdb=" CB ASP C 191 " pdb=" CG ASP C 191 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.16e+00 bond pdb=" CB ASP B 191 " pdb=" CG ASP B 191 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.14e+00 bond pdb=" CA VAL A 175 " pdb=" CB VAL A 175 " ideal model delta sigma weight residual 1.527 1.546 -0.020 1.31e-02 5.83e+03 2.24e+00 bond pdb=" CA VAL C 175 " pdb=" CB VAL C 175 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.17e+00 ... (remaining 6733 not shown) Histogram of bond angle deviations from ideal: 81.09 - 91.13: 9 91.13 - 101.18: 6 101.18 - 111.22: 7265 111.22 - 121.26: 3348 121.26 - 131.31: 1441 Bond angle restraints: 12069 Sorted by residual: angle pdb=" CG2 THR A 235 " pdb=" CB THR A 235 " pdb=" HB THR A 235 " ideal model delta sigma weight residual 108.00 81.09 26.91 3.00e+00 1.11e-01 8.05e+01 angle pdb=" CG2 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 108.00 81.14 26.86 3.00e+00 1.11e-01 8.02e+01 angle pdb=" CG2 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 108.00 81.16 26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" OG1 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 109.00 82.96 26.04 3.00e+00 1.11e-01 7.53e+01 angle pdb=" OG1 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 109.00 83.02 25.98 3.00e+00 1.11e-01 7.50e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2281 16.15 - 32.31: 374 32.31 - 48.46: 60 48.46 - 64.61: 30 64.61 - 80.77: 15 Dihedral angle restraints: 2760 sinusoidal: 1329 harmonic: 1431 Sorted by residual: dihedral pdb=" CA ALA A 204 " pdb=" C ALA A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA C 204 " pdb=" C ALA C 204 " pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA B 204 " pdb=" C ALA B 204 " pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 2757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 597 0.293 - 0.585: 3 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 3 Chirality restraints: 603 Sorted by residual: chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR B 235 " pdb=" CA THR B 235 " pdb=" OG1 THR B 235 " pdb=" CG2 THR B 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 ... (remaining 600 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 145 " -0.037 2.00e-02 2.50e+03 2.83e-02 1.20e+01 pdb=" CG ASN A 145 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN A 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.037 2.00e-02 2.50e+03 2.82e-02 1.19e+01 pdb=" CG ASN C 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.19e+01 pdb=" CG ASN B 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN B 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " -0.037 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 483 2.19 - 2.79: 13507 2.79 - 3.40: 17849 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91124 Sorted by model distance: nonbonded pdb=" H VAL B 128 " pdb=" O VAL C 128 " model vdw 1.591 1.850 nonbonded pdb=" O VAL B 128 " pdb=" H VAL A 128 " model vdw 1.612 1.850 nonbonded pdb=" OG SER B 240 " pdb=" HH TYR C 236 " model vdw 1.663 1.850 nonbonded pdb=" HH TYR B 236 " pdb=" OG SER A 240 " model vdw 1.680 1.850 nonbonded pdb=" O GLU B 205 " pdb=" H GLU C 206 " model vdw 1.745 1.850 ... (remaining 91119 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: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 H 3255 0.53 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: 0.710 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: 0.090 Extract box with map and model: 4.370 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 25.490 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 : 0.006 0.045 3483 Z= 0.379 Angle : 1.179 11.646 4737 Z= 0.676 Chirality : 0.123 1.463 603 Planarity : 0.009 0.056 573 Dihedral : 17.368 69.314 1281 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -6.51 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.21), 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 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 1.2814 time to fit residues: 125.5569 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1468 time to fit residues: 0.9229 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 223 ASN B 242 GLN A 154 ASN A 223 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN C 155 ASN C 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 3483 Z= 0.404 Angle : 0.867 11.784 4737 Z= 0.487 Chirality : 0.116 1.576 603 Planarity : 0.007 0.070 573 Dihedral : 7.131 31.931 522 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.06 % Favored : 76.94 % Rotamer Outliers : 10.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -6.33 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.82 (0.22), 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 130 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.516 Fit side-chains outliers start: 38 outliers final: 9 residues processed: 116 average time/residue: 1.3269 time to fit residues: 161.3173 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.7152 time to fit residues: 2.2129 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN A 154 ASN C 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3483 Z= 0.274 Angle : 0.716 11.485 4737 Z= 0.409 Chirality : 0.111 1.440 603 Planarity : 0.005 0.056 573 Dihedral : 6.677 30.985 522 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer Outliers : 6.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -6.03 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.23), 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 109 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.572 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 102 average time/residue: 1.3860 time to fit residues: 148.0508 Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.5290 time to fit residues: 2.4155 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3483 Z= 0.196 Angle : 0.654 11.338 4737 Z= 0.372 Chirality : 0.109 1.411 603 Planarity : 0.004 0.051 573 Dihedral : 6.176 25.963 522 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer Outliers : 5.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.84 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.23), 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 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.517 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 1.2273 time to fit residues: 125.3661 Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.0754 time to fit residues: 1.2170 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3483 Z= 0.236 Angle : 0.660 11.380 4737 Z= 0.376 Chirality : 0.110 1.426 603 Planarity : 0.004 0.050 573 Dihedral : 6.097 22.058 522 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.71 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.24), 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 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 101 average time/residue: 1.2179 time to fit residues: 129.5055 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.0750 time to fit residues: 1.0953 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3483 Z= 0.183 Angle : 0.636 11.344 4737 Z= 0.360 Chirality : 0.109 1.418 603 Planarity : 0.004 0.047 573 Dihedral : 5.916 17.020 522 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.58 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.24), 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 105 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 100 average time/residue: 1.1623 time to fit residues: 122.7904 Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.0752 time to fit residues: 1.2046 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.7334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3483 Z= 0.189 Angle : 0.638 11.348 4737 Z= 0.360 Chirality : 0.109 1.415 603 Planarity : 0.003 0.046 573 Dihedral : 5.842 15.945 522 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer Outliers : 7.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.48 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.24), 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 112 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 103 average time/residue: 1.1964 time to fit residues: 130.0294 Evaluate side-chains 101 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.0753 time to fit residues: 1.2069 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3483 Z= 0.251 Angle : 0.669 11.411 4737 Z= 0.379 Chirality : 0.110 1.425 603 Planarity : 0.004 0.054 573 Dihedral : 5.926 16.244 522 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer Outliers : 5.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.48 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.24), 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 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 1.2339 time to fit residues: 130.0811 Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0758 time to fit residues: 0.8120 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3483 Z= 0.189 Angle : 0.647 11.334 4737 Z= 0.366 Chirality : 0.109 1.404 603 Planarity : 0.004 0.052 573 Dihedral : 5.813 15.813 522 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.42 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.24), 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 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 1.2498 time to fit residues: 128.9166 Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.4794 time to fit residues: 2.8145 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3483 Z= 0.209 Angle : 0.649 11.510 4737 Z= 0.367 Chirality : 0.110 1.443 603 Planarity : 0.004 0.056 573 Dihedral : 5.792 15.706 522 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.34 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.24), 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 99 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 1.1205 time to fit residues: 113.7746 Evaluate side-chains 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0738 time to fit residues: 0.9076 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.211860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.191289 restraints weight = 11617.235| |-----------------------------------------------------------------------------| r_work (start): 0.4806 rms_B_bonded: 2.22 r_work: 0.4796 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4788 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.4779 rms_B_bonded: 2.05 restraints_weight: 0.1250 r_work: 0.4770 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.4760 rms_B_bonded: 2.31 restraints_weight: 0.0312 r_work: 0.4748 rms_B_bonded: 2.52 restraints_weight: 0.0156 r_work: 0.4735 rms_B_bonded: 2.79 restraints_weight: 0.0078 r_work: 0.4720 rms_B_bonded: 3.14 restraints_weight: 0.0039 r_work: 0.4703 rms_B_bonded: 3.57 restraints_weight: 0.0020 r_work: 0.4684 rms_B_bonded: 4.10 restraints_weight: 0.0010 r_work: 0.4662 rms_B_bonded: 4.75 restraints_weight: 0.0005 r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3483 Z= 0.163 Angle : 0.628 11.336 4737 Z= 0.354 Chirality : 0.109 1.420 603 Planarity : 0.004 0.056 573 Dihedral : 5.677 15.580 522 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.23 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 399 =============================================================================== Job complete usr+sys time: 3771.27 seconds wall clock time: 66 minutes 36.94 seconds (3996.94 seconds total)