Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/11_2022/7w3t_32293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/11_2022/7w3t_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_32293/11_2022/7w3t_32293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/11_2022/7w3t_32293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/11_2022/7w3t_32293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/11_2022/7w3t_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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 dihedrals: 1 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: 1.55, per 1000 atoms: 1.07 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: 0.87 Conformation dependent library (CDL) restraints added in 228.1 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: 0.12 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: 0.34 Time building geometry restraints manager: 0.83 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=" CB CYS B 60 " pdb=" SG CYS B 60 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.17e-01 bond pdb=" CB CYS B 67 " pdb=" SG CYS B 67 " ideal model delta sigma weight residual 1.808 1.782 0.026 3.30e-02 9.18e+02 6.24e-01 bond pdb=" CA PRO B 134 " pdb=" C PRO B 134 " ideal model delta sigma weight residual 1.525 1.519 0.007 9.70e-03 1.06e+04 4.59e-01 bond pdb=" CB ASN B 151 " pdb=" CG ASN B 151 " ideal model delta sigma weight residual 1.516 1.503 0.013 2.50e-02 1.60e+03 2.59e-01 bond pdb=" CG LEU B 83 " pdb=" CD1 LEU B 83 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.48e-01 ... (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=" 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 angle pdb=" C THR B 61 " pdb=" N TRP B 62 " pdb=" CA TRP B 62 " ideal model delta sigma weight residual 120.71 123.09 -2.38 1.42e+00 4.96e-01 2.82e+00 ... (remaining 2024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 775 15.06 - 30.12: 83 30.12 - 45.18: 26 45.18 - 60.24: 3 60.24 - 75.30: 2 Dihedral angle restraints: 889 sinusoidal: 381 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 886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 167 0.036 - 0.071: 67 0.071 - 0.107: 20 0.107 - 0.143: 7 0.143 - 0.178: 3 Chirality restraints: 264 Sorted by residual: 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 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 117 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.19e-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 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. 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: 0.510 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: 2.840 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.010 Process input model: 10.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.003 0.030 1481 Z= 0.192 Angle : 0.596 7.147 2029 Z= 0.306 Chirality : 0.046 0.178 264 Planarity : 0.006 0.040 258 Dihedral : 13.928 75.298 556 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 : 0.167 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1089 time to fit residues: 5.2273 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2350 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 1481 Z= 0.327 Angle : 0.689 10.152 2029 Z= 0.339 Chirality : 0.049 0.208 264 Planarity : 0.006 0.034 258 Dihedral : 5.389 15.465 230 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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: -3.23 (0.60), residues: 174 helix: -3.12 (0.62), residues: 44 sheet: -2.85 (0.87), residues: 29 loop : -1.39 (0.62), 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 : 0.176 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.0987 time to fit residues: 5.0336 Evaluate side-chains 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.175 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0193 time to fit residues: 0.2902 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 12 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 1481 Z= 0.258 Angle : 0.628 7.091 2029 Z= 0.317 Chirality : 0.047 0.201 264 Planarity : 0.006 0.039 258 Dihedral : 5.392 17.341 230 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -3.33 (0.60), residues: 174 helix: -3.38 (0.60), residues: 44 sheet: -2.90 (0.86), residues: 29 loop : -1.36 (0.62), 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 43 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.163 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 43 average time/residue: 0.0976 time to fit residues: 5.0167 Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2451 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.0570 chunk 8 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 0.0570 chunk 11 optimal weight: 0.1980 overall best weight: 0.1014 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 1481 Z= 0.163 Angle : 0.591 5.328 2029 Z= 0.299 Chirality : 0.046 0.191 264 Planarity : 0.005 0.037 258 Dihedral : 5.121 16.911 230 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -3.25 (0.61), residues: 174 helix: -3.28 (0.63), residues: 44 sheet: -3.07 (0.93), residues: 26 loop : -1.33 (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 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.163 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1041 time to fit residues: 4.8042 Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.164 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0181 time to fit residues: 0.2541 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 1481 Z= 0.304 Angle : 0.639 5.349 2029 Z= 0.327 Chirality : 0.047 0.200 264 Planarity : 0.005 0.036 258 Dihedral : 5.366 15.883 230 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -3.30 (0.61), residues: 174 helix: -3.32 (0.62), residues: 44 sheet: -3.17 (0.91), residues: 27 loop : -1.32 (0.62), residues: 103 *********************** 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 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.164 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.0967 time to fit residues: 4.9378 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.164 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0201 time to fit residues: 0.2580 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 6 optimal weight: 0.0370 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.1544 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= 0.211 Angle : 0.586 5.705 2029 Z= 0.294 Chirality : 0.046 0.196 264 Planarity : 0.005 0.033 258 Dihedral : 5.232 16.134 230 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.37 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: -3.27 (0.61), residues: 174 helix: -3.25 (0.64), residues: 44 sheet: -3.23 (0.90), residues: 27 loop : -1.30 (0.62), residues: 103 *********************** 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 43 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.173 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.1009 time to fit residues: 5.0760 Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.178 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0234 time to fit residues: 0.2716 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 1481 Z= 0.327 Angle : 0.650 5.736 2029 Z= 0.326 Chirality : 0.049 0.209 264 Planarity : 0.005 0.034 258 Dihedral : 5.501 16.091 230 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -3.38 (0.60), residues: 174 helix: -3.42 (0.60), residues: 44 sheet: -3.18 (0.93), residues: 27 loop : -1.37 (0.61), residues: 103 *********************** 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 45 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.170 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1007 time to fit residues: 5.0992 Evaluate side-chains 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.147 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0309 time to fit residues: 0.2917 ------------------------------------------------------------------------------- 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: 0.1980 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.1709 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= 0.206 Angle : 0.610 6.276 2029 Z= 0.305 Chirality : 0.046 0.192 264 Planarity : 0.005 0.032 258 Dihedral : 5.271 15.375 230 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.02 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: -3.27 (0.62), residues: 174 helix: -3.26 (0.64), residues: 44 sheet: -3.23 (0.93), residues: 27 loop : -1.28 (0.63), residues: 103 *********************** 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 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.165 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1003 time to fit residues: 4.6478 Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2354 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0040 chunk 12 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 0.2980 overall best weight: 0.1908 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 1481 Z= 0.183 Angle : 0.587 6.601 2029 Z= 0.290 Chirality : 0.045 0.192 264 Planarity : 0.005 0.030 258 Dihedral : 5.184 15.195 230 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.02 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: -3.11 (0.63), residues: 174 helix: -3.16 (0.65), residues: 44 sheet: -3.10 (0.97), residues: 27 loop : -1.17 (0.64), residues: 103 *********************** 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 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.169 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1019 time to fit residues: 4.7045 Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0417 time to fit residues: 0.2752 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1729 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= 0.221 Angle : 0.602 6.676 2029 Z= 0.295 Chirality : 0.046 0.193 264 Planarity : 0.005 0.031 258 Dihedral : 5.199 14.931 230 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -3.12 (0.63), residues: 174 helix: -3.17 (0.65), residues: 44 sheet: -3.09 (0.97), residues: 27 loop : -1.19 (0.64), residues: 103 ********************** 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 38 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1061 time to fit residues: 4.7451 Evaluate side-chains 38 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2276 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106157 restraints weight = 2218.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109605 restraints weight = 1253.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111957 restraints weight = 832.551| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1769 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= 0.232 Angle : 0.619 6.888 2029 Z= 0.308 Chirality : 0.047 0.191 264 Planarity : 0.005 0.031 258 Dihedral : 5.323 15.655 230 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -3.15 (0.62), residues: 174 helix: -3.17 (0.65), residues: 44 sheet: -3.15 (0.96), residues: 27 loop : -1.21 (0.64), residues: 103 =============================================================================== Job complete usr+sys time: 991.00 seconds wall clock time: 18 minutes 7.84 seconds (1087.84 seconds total)