Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:53:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/11_2022/6mlu_9146.pdb" } resolution = 4.0 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 1.96, per 1000 atoms: 0.78 Number of scatterers: 2516 At special positions: 0 Unit cell: (72.05, 73.36, 58.95, 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 28 16.00 O 446 8.00 N 426 7.00 C 1616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 164 " distance=2.04 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: 0.91 Conformation dependent library (CDL) restraints added in 336.0 milliseconds 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 596 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 24.2% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 4.585A pdb=" N VAL A 232 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 231 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG A 153 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.583A pdb=" N VAL B 232 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 231 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 153 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 300 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: 0.58 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 796 1.34 - 1.46: 577 1.46 - 1.58: 1159 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2580 Sorted by residual: bond pdb=" CA HIS A 110 " pdb=" CB HIS A 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.91e+00 bond pdb=" CA HIS B 110 " pdb=" CB HIS B 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.89e+00 bond pdb=" CA ARG A 88 " pdb=" C ARG A 88 " ideal model delta sigma weight residual 1.525 1.555 -0.030 2.10e-02 2.27e+03 2.02e+00 bond pdb=" CA ARG B 88 " pdb=" C ARG B 88 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.10e-02 2.27e+03 1.88e+00 bond pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 ... (remaining 2575 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 81 105.65 - 112.73: 1335 112.73 - 119.81: 849 119.81 - 126.89: 1178 126.89 - 133.97: 51 Bond angle restraints: 3494 Sorted by residual: angle pdb=" C ALA A 109 " pdb=" N HIS A 110 " pdb=" CA HIS A 110 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ALA B 109 " pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C LEU B 98 " pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C LEU A 98 " pdb=" N GLU A 99 " pdb=" CA GLU A 99 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C LEU B 208 " pdb=" N GLU B 209 " pdb=" CA GLU B 209 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 3489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.37: 1401 11.37 - 22.73: 135 22.73 - 34.09: 24 34.09 - 45.46: 12 45.46 - 56.82: 6 Dihedral angle restraints: 1578 sinusoidal: 664 harmonic: 914 Sorted by residual: dihedral pdb=" CA HIS B 110 " pdb=" C HIS B 110 " pdb=" N VAL B 111 " pdb=" CA VAL B 111 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA HIS A 110 " pdb=" C HIS A 110 " pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA TRP A 192 " pdb=" C TRP A 192 " pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 277 0.055 - 0.109: 74 0.109 - 0.164: 28 0.164 - 0.218: 7 0.218 - 0.273: 2 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA HIS B 110 " pdb=" N HIS B 110 " pdb=" C HIS B 110 " pdb=" CB HIS B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA HIS A 110 " pdb=" N HIS A 110 " pdb=" C HIS A 110 " pdb=" CB HIS A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB THR B 100 " pdb=" CA THR B 100 " pdb=" OG1 THR B 100 " pdb=" CG2 THR B 100 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 385 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 209 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C GLU B 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU B 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU B 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 209 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C GLU A 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 109 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ALA B 109 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 109 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 110 " 0.010 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 921 2.90 - 3.40: 2472 3.40 - 3.90: 4091 3.90 - 4.40: 4488 4.40 - 4.90: 7629 Nonbonded interactions: 19601 Sorted by model distance: nonbonded pdb=" OD1 ASP A 154 " pdb=" N MET A 158 " model vdw 2.406 2.520 nonbonded pdb=" OD1 ASP B 154 " pdb=" N MET B 158 " model vdw 2.409 2.520 nonbonded pdb=" NH1 ARG B 206 " pdb=" O PHE B 240 " model vdw 2.415 2.520 nonbonded pdb=" NH1 ARG A 206 " pdb=" O PHE A 240 " model vdw 2.415 2.520 nonbonded pdb=" OH TYR A 230 " pdb=" N TYR B 171 " model vdw 2.432 2.520 ... (remaining 19596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1616 2.51 5 N 426 2.21 5 O 446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 3.710 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.080 Find NCS groups from input model: 0.120 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.005 0.044 2580 Z= 0.345 Angle : 1.046 10.429 3494 Z= 0.564 Chirality : 0.064 0.273 388 Planarity : 0.007 0.036 440 Dihedral : 9.856 47.411 976 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer Outliers : 0.69 % 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: -4.38 (0.42), residues: 302 helix: -2.79 (0.45), residues: 74 sheet: -1.76 (0.57), residues: 86 loop : -3.75 (0.42), residues: 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.2068 time to fit residues: 37.3609 Evaluate side-chains 115 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 2580 Z= 0.223 Angle : 0.813 7.047 3494 Z= 0.429 Chirality : 0.055 0.210 388 Planarity : 0.005 0.031 440 Dihedral : 6.234 23.330 336 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer Outliers : 7.29 % 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: -3.20 (0.46), residues: 302 helix: -0.48 (0.59), residues: 74 sheet: -1.72 (0.52), residues: 90 loop : -3.38 (0.48), residues: 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 137 average time/residue: 0.1820 time to fit residues: 28.2555 Evaluate side-chains 122 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0321 time to fit residues: 0.9274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 140 ASN B 124 GLN B 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2580 Z= 0.229 Angle : 0.810 7.161 3494 Z= 0.423 Chirality : 0.054 0.271 388 Planarity : 0.005 0.029 440 Dihedral : 6.127 22.043 336 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 6.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.46), residues: 302 helix: 0.02 (0.58), residues: 74 sheet: -2.00 (0.48), residues: 96 loop : -3.11 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.2004 time to fit residues: 27.4543 Evaluate side-chains 113 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0309 time to fit residues: 0.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 0.0040 chunk 7 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 0 optimal weight: 0.9980 overall best weight: 1.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 2580 Z= 0.228 Angle : 0.794 7.521 3494 Z= 0.412 Chirality : 0.055 0.304 388 Planarity : 0.005 0.033 440 Dihedral : 6.080 21.947 336 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.46), residues: 302 helix: 0.17 (0.56), residues: 74 sheet: -1.84 (0.49), residues: 94 loop : -2.96 (0.51), residues: 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 121 average time/residue: 0.1993 time to fit residues: 27.0087 Evaluate side-chains 120 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0332 time to fit residues: 0.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 2580 Z= 0.306 Angle : 0.863 8.635 3494 Z= 0.446 Chirality : 0.057 0.403 388 Planarity : 0.005 0.041 440 Dihedral : 6.255 22.156 336 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 30.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 6.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.48), residues: 302 helix: 0.73 (0.62), residues: 74 sheet: -1.69 (0.52), residues: 90 loop : -3.20 (0.49), residues: 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 124 average time/residue: 0.1968 time to fit residues: 27.3089 Evaluate side-chains 119 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0358 time to fit residues: 0.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.0870 chunk 21 optimal weight: 8.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 197 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 2580 Z= 0.235 Angle : 0.869 9.574 3494 Z= 0.438 Chirality : 0.056 0.338 388 Planarity : 0.005 0.032 440 Dihedral : 6.158 23.089 336 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.47), residues: 302 helix: 0.62 (0.62), residues: 72 sheet: -1.56 (0.52), residues: 90 loop : -3.29 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 119 average time/residue: 0.1893 time to fit residues: 25.4803 Evaluate side-chains 121 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0353 time to fit residues: 0.8210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 2580 Z= 0.281 Angle : 0.938 10.695 3494 Z= 0.464 Chirality : 0.058 0.360 388 Planarity : 0.005 0.034 440 Dihedral : 6.246 23.043 336 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.48), residues: 302 helix: 0.53 (0.62), residues: 74 sheet: -1.88 (0.50), residues: 94 loop : -3.07 (0.51), residues: 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 118 average time/residue: 0.1836 time to fit residues: 24.6212 Evaluate side-chains 114 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0343 time to fit residues: 0.5971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 235 HIS ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 2580 Z= 0.234 Angle : 0.902 10.310 3494 Z= 0.449 Chirality : 0.057 0.372 388 Planarity : 0.005 0.036 440 Dihedral : 6.093 22.391 336 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.47), residues: 302 helix: 0.68 (0.62), residues: 72 sheet: -1.84 (0.49), residues: 94 loop : -3.15 (0.51), residues: 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 0.1798 time to fit residues: 25.3697 Evaluate side-chains 121 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0442 time to fit residues: 0.7557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.7779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 2580 Z= 0.294 Angle : 0.971 13.468 3494 Z= 0.482 Chirality : 0.059 0.379 388 Planarity : 0.006 0.044 440 Dihedral : 6.186 22.398 336 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 32.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.48), residues: 302 helix: 0.81 (0.65), residues: 74 sheet: -1.74 (0.49), residues: 94 loop : -3.10 (0.51), residues: 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 118 average time/residue: 0.1885 time to fit residues: 25.1100 Evaluate side-chains 117 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0275 time to fit residues: 0.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 197 GLN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 2580 Z= 0.263 Angle : 1.001 13.175 3494 Z= 0.499 Chirality : 0.058 0.394 388 Planarity : 0.006 0.052 440 Dihedral : 6.180 22.540 336 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.48), residues: 302 helix: 0.71 (0.64), residues: 72 sheet: -1.74 (0.50), residues: 94 loop : -3.16 (0.51), residues: 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 120 average time/residue: 0.1810 time to fit residues: 24.6677 Evaluate side-chains 117 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0502 time to fit residues: 0.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094607 restraints weight = 7381.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097213 restraints weight = 4228.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098900 restraints weight = 2962.403| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 2580 Z= 0.324 Angle : 1.048 12.527 3494 Z= 0.521 Chirality : 0.062 0.390 388 Planarity : 0.006 0.049 440 Dihedral : 6.542 22.932 336 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.48), residues: 302 helix: 0.56 (0.63), residues: 74 sheet: -1.58 (0.53), residues: 90 loop : -3.18 (0.49), residues: 138 =============================================================================== Job complete usr+sys time: 1038.44 seconds wall clock time: 20 minutes 16.17 seconds (1216.17 seconds total)