Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 16:24:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/07_2023/7w3t_32293.pdb" } resolution = 3.59 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= 0.012 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 915 2.51 5 N 241 2.21 5 O 296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 1455 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1360 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 1.43, per 1000 atoms: 0.98 Number of scatterers: 1455 At special positions: 0 Unit cell: (66.843, 46.684, 55.172, 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 3 16.00 O 296 8.00 N 241 7.00 C 915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 67 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN B 186 " " NAG B1000 " - " ASN B 82 " " NAG B1001 " - " ASN B 106 " " NAG B1002 " - " ASN B 117 " " NAG B1003 " - " ASN B 152 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 229.0 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 3 sheets defined 27.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.574A pdb=" N GLN B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.819A pdb=" N LEU B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.565A pdb=" N VAL B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.503A pdb=" N PHE B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.402A pdb=" N GLY B 85 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE B 107 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.383A pdb=" N VAL B 76 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 100 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 124 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASN B 151 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 148 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 175 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158 removed outlier: 6.452A pdb=" N GLY B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 27 hydrogen bonds defined for protein. 39 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: 0.29 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: 475 1.34 - 1.46: 267 1.46 - 1.57: 735 1.57 - 1.69: 0 1.69 - 1.81: 4 Bond restraints: 1481 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.545 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 1476 not shown) Histogram of bond angle deviations from ideal: 101.83 - 108.25: 89 108.25 - 114.67: 896 114.67 - 121.09: 586 121.09 - 127.51: 447 127.51 - 133.92: 11 Bond angle restraints: 2029 Sorted by residual: angle pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N ILE B 135 " ideal model delta sigma weight residual 114.74 116.95 -2.21 1.03e+00 9.43e-01 4.62e+00 angle pdb=" C3 BMA A 3 " pdb=" C2 BMA A 3 " pdb=" O2 BMA A 3 " ideal model delta sigma weight residual 112.95 106.58 6.37 3.00e+00 1.11e-01 4.50e+00 angle pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " pdb=" CG LEU B 162 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA CYS B 60 " pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " ideal model delta sigma weight residual 114.40 109.82 4.58 2.30e+00 1.89e-01 3.96e+00 angle pdb=" C LYS B 144 " pdb=" N LEU B 145 " pdb=" CA LEU B 145 " ideal model delta sigma weight residual 122.74 119.46 3.28 1.82e+00 3.02e-01 3.26e+00 ... (remaining 2024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 729 15.06 - 30.12: 83 30.12 - 45.18: 26 45.18 - 60.24: 3 60.24 - 75.30: 2 Dihedral angle restraints: 843 sinusoidal: 335 harmonic: 508 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 132.69 -39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA CYS B 67 " pdb=" C CYS B 67 " pdb=" N ASN B 68 " pdb=" CA ASN B 68 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU B 70 " pdb=" C GLU B 70 " pdb=" N ASN B 71 " pdb=" CA ASN B 71 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 209 0.055 - 0.110: 44 0.110 - 0.165: 7 0.165 - 0.220: 3 0.220 - 0.275: 1 Chirality restraints: 264 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B1000 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B1000 " pdb=" O5 NAG B1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 106 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 261 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 62 " 0.018 2.00e-02 2.50e+03 1.86e-02 8.63e+00 pdb=" CG TRP B 62 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 62 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 62 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 62 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 62 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 62 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 62 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 159 " -0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 160 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO B 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 321 2.79 - 3.32: 1407 3.32 - 3.84: 2237 3.84 - 4.37: 2594 4.37 - 4.90: 4242 Nonbonded interactions: 10801 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" OG SER B 72 " model vdw 2.259 2.440 nonbonded pdb=" O LEU B 162 " pdb=" OG1 THR B 165 " model vdw 2.278 2.440 nonbonded pdb=" O GLY B 187 " pdb=" OG SER B 190 " model vdw 2.338 2.440 nonbonded pdb=" O LEU B 145 " pdb=" OG SER B 168 " model vdw 2.366 2.440 nonbonded pdb=" O GLY B 85 " pdb=" N SER B 108 " model vdw 2.389 2.520 ... (remaining 10796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.590 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: 0.010 Extract box with map and model: 2.880 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.004 0.033 1481 Z= 0.256 Angle : 0.731 7.147 2029 Z= 0.335 Chirality : 0.052 0.275 264 Planarity : 0.006 0.040 258 Dihedral : 14.392 75.298 510 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.63), residues: 174 helix: -2.58 (0.70), residues: 44 sheet: -2.90 (0.90), residues: 28 loop : -1.17 (0.65), residues: 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.151 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1108 time to fit residues: 5.2988 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 1481 Z= 0.273 Angle : 0.679 10.058 2029 Z= 0.325 Chirality : 0.049 0.209 264 Planarity : 0.006 0.035 258 Dihedral : 4.774 15.257 184 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.61), residues: 174 helix: -2.99 (0.64), residues: 44 sheet: -2.84 (0.88), residues: 29 loop : -1.34 (0.63), residues: 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.162 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1108 time to fit residues: 5.5972 Evaluate side-chains 46 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.166 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0201 time to fit residues: 0.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 5 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 1481 Z= 0.211 Angle : 0.622 7.135 2029 Z= 0.307 Chirality : 0.048 0.207 264 Planarity : 0.005 0.038 258 Dihedral : 4.731 16.354 184 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.61), residues: 174 helix: -3.30 (0.63), residues: 44 sheet: -2.84 (0.87), residues: 29 loop : -1.29 (0.63), residues: 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.154 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.1051 time to fit residues: 4.9774 Evaluate side-chains 38 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.0000 chunk 11 optimal weight: 0.0970 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 1481 Z= 0.272 Angle : 0.659 5.540 2029 Z= 0.330 Chirality : 0.050 0.211 264 Planarity : 0.005 0.038 258 Dihedral : 4.882 17.339 184 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 2.50 % 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: -3.34 (0.61), residues: 174 helix: -3.34 (0.61), residues: 44 sheet: -3.44 (0.89), residues: 26 loop : -1.30 (0.62), residues: 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.166 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1068 time to fit residues: 5.1686 Evaluate side-chains 45 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.167 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0200 time to fit residues: 0.2912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 1481 Z= 0.270 Angle : 0.655 5.407 2029 Z= 0.329 Chirality : 0.049 0.204 264 Planarity : 0.005 0.037 258 Dihedral : 4.861 17.025 184 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.61), residues: 174 helix: -3.27 (0.63), residues: 44 sheet: -3.46 (0.90), residues: 26 loop : -1.30 (0.62), residues: 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1100 time to fit residues: 5.4699 Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 6 optimal weight: 0.0070 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 1481 Z= 0.181 Angle : 0.600 5.581 2029 Z= 0.295 Chirality : 0.048 0.235 264 Planarity : 0.005 0.034 258 Dihedral : 4.553 17.391 184 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 1.88 % 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: -3.19 (0.61), residues: 174 helix: -3.11 (0.66), residues: 44 sheet: -3.36 (0.95), residues: 25 loop : -1.28 (0.62), residues: 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.162 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.1058 time to fit residues: 5.2377 Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 10 optimal weight: 0.0770 chunk 11 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.0270 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 1481 Z= 0.174 Angle : 0.609 6.901 2029 Z= 0.294 Chirality : 0.048 0.219 264 Planarity : 0.005 0.032 258 Dihedral : 4.466 17.285 184 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.62 % 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: -3.04 (0.63), residues: 174 helix: -2.98 (0.69), residues: 44 sheet: -3.19 (0.86), residues: 30 loop : -1.07 (0.65), residues: 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.166 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1103 time to fit residues: 5.0305 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0181 time to fit residues: 0.2520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.0000 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 1481 Z= 0.192 Angle : 0.609 6.075 2029 Z= 0.294 Chirality : 0.048 0.213 264 Planarity : 0.005 0.030 258 Dihedral : 4.443 15.508 184 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.64), residues: 174 helix: -2.91 (0.70), residues: 44 sheet: -3.26 (0.84), residues: 31 loop : -0.93 (0.67), residues: 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.153 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1063 time to fit residues: 5.0107 Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 0.2980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 1481 Z= 0.181 Angle : 0.604 6.349 2029 Z= 0.290 Chirality : 0.048 0.212 264 Planarity : 0.005 0.029 258 Dihedral : 4.533 16.701 184 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.62 % 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: -2.92 (0.64), residues: 174 helix: -2.87 (0.71), residues: 44 sheet: -3.25 (0.84), residues: 31 loop : -0.90 (0.67), residues: 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.176 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1045 time to fit residues: 4.9005 Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0405 time to fit residues: 0.2515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 6 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.0670 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 1481 Z= 0.210 Angle : 0.619 6.829 2029 Z= 0.298 Chirality : 0.048 0.213 264 Planarity : 0.005 0.030 258 Dihedral : 4.489 14.961 184 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.62 % 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: -2.92 (0.64), residues: 174 helix: -2.88 (0.70), residues: 44 sheet: -3.10 (0.88), residues: 30 loop : -0.99 (0.66), residues: 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1032 time to fit residues: 4.9714 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.151 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0194 time to fit residues: 0.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.0060 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107822 restraints weight = 2231.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111341 restraints weight = 1250.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113606 restraints weight = 830.035| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 1481 Z= 0.167 Angle : 0.601 7.017 2029 Z= 0.287 Chirality : 0.048 0.209 264 Planarity : 0.005 0.032 258 Dihedral : 4.439 15.805 184 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.62 % 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: -2.89 (0.65), residues: 174 helix: -2.83 (0.71), residues: 44 sheet: -3.24 (0.84), residues: 31 loop : -0.89 (0.67), residues: 99 =============================================================================== Job complete usr+sys time: 1048.29 seconds wall clock time: 19 minutes 6.33 seconds (1146.33 seconds total)