Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:30:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9m_16511/02_2023/8c9m_16511.pdb" } resolution = 3.2 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= 0.031 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 Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "B" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "C" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "D" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "E" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "F" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3580 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Time building chain proxies: 10.60, per 1000 atoms: 0.49 Number of scatterers: 21480 At special positions: 0 Unit cell: (121.743, 121.743, 96.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2004 8.00 N 1890 7.00 C 6762 6.00 H 10752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 56 through 80 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 147 through 163 Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 56 through 80 Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 147 through 163 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 56 through 80 Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 109 through 126 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 147 through 163 Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 56 through 80 Processing helix chain 'D' and resid 88 through 94 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 147 through 163 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.214A pdb=" N ALA D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'E' and resid 9 through 23 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 56 through 80 Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 109 through 126 Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 147 through 163 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'E' and resid 215 through 228 Processing helix chain 'F' and resid 9 through 23 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 43 through 53 Processing helix chain 'F' and resid 56 through 80 Processing helix chain 'F' and resid 88 through 94 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 109 through 126 Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 147 through 163 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 182 through 190 removed outlier: 4.213A pdb=" N ALA F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 215 through 228 696 hydrogen bonds defined for protein. 2052 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: 7.25 Time building geometry restraints manager: 19.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 10728 1.11 - 1.29: 1939 1.29 - 1.46: 3905 1.46 - 1.63: 5010 1.63 - 1.81: 120 Bond restraints: 21702 Sorted by residual: bond pdb=" CA TRP F 67 " pdb=" C TRP F 67 " ideal model delta sigma weight residual 1.524 1.386 0.138 1.27e-02 6.20e+03 1.18e+02 bond pdb=" CA TRP B 67 " pdb=" C TRP B 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP D 67 " pdb=" C TRP D 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP A 67 " pdb=" C TRP A 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 bond pdb=" CA TRP C 67 " pdb=" C TRP C 67 " ideal model delta sigma weight residual 1.524 1.386 0.137 1.27e-02 6.20e+03 1.17e+02 ... (remaining 21697 not shown) Histogram of bond angle deviations from ideal: 93.14 - 101.32: 55 101.32 - 109.50: 16005 109.50 - 117.68: 12262 117.68 - 125.86: 10765 125.86 - 134.04: 255 Bond angle restraints: 39342 Sorted by residual: angle pdb=" C GLY E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta sigma weight residual 119.32 128.46 -9.14 1.14e+00 7.69e-01 6.43e+01 angle pdb=" C GLY D 23 " pdb=" N PRO D 24 " pdb=" CA PRO D 24 " ideal model delta sigma weight residual 119.32 128.44 -9.12 1.14e+00 7.69e-01 6.40e+01 angle pdb=" C GLY C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta sigma weight residual 119.32 128.43 -9.11 1.14e+00 7.69e-01 6.39e+01 angle pdb=" C GLY F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta sigma weight residual 119.32 128.42 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" C GLY A 23 " pdb=" N PRO A 24 " pdb=" CA PRO A 24 " ideal model delta sigma weight residual 119.32 128.42 -9.10 1.14e+00 7.69e-01 6.37e+01 ... (remaining 39337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 8419 14.79 - 29.58: 167 29.58 - 44.38: 41 44.38 - 59.17: 31 59.17 - 73.96: 6 Dihedral angle restraints: 8664 sinusoidal: 4128 harmonic: 4536 Sorted by residual: dihedral pdb=" CD2 HIS C 40 " pdb=" CG HIS C 40 " pdb=" ND1 HIS C 40 " pdb=" HD1 HIS C 40 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CD2 HIS F 40 " pdb=" CG HIS F 40 " pdb=" ND1 HIS F 40 " pdb=" HD1 HIS F 40 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CD2 HIS E 40 " pdb=" CG HIS E 40 " pdb=" ND1 HIS E 40 " pdb=" HD1 HIS E 40 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 784 0.073 - 0.147: 475 0.147 - 0.220: 273 0.220 - 0.293: 46 0.293 - 0.367: 18 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA TRP C 67 " pdb=" N TRP C 67 " pdb=" C TRP C 67 " pdb=" CB TRP C 67 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP D 67 " pdb=" N TRP D 67 " pdb=" C TRP D 67 " pdb=" CB TRP D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP A 67 " pdb=" N TRP A 67 " pdb=" C TRP A 67 " pdb=" CB TRP A 67 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1593 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 40 " -0.100 2.00e-02 2.50e+03 9.60e-02 2.08e+02 pdb=" CG HIS C 40 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS C 40 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS C 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS C 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS C 40 " 0.221 2.00e-02 2.50e+03 pdb=" HD2 HIS C 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS C 40 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 40 " -0.100 2.00e-02 2.50e+03 9.60e-02 2.07e+02 pdb=" CG HIS F 40 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS F 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS F 40 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS F 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS F 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS F 40 " 0.221 2.00e-02 2.50e+03 pdb=" HD2 HIS F 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS F 40 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 40 " -0.100 2.00e-02 2.50e+03 9.58e-02 2.06e+02 pdb=" CG HIS E 40 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS E 40 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 HIS E 40 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS E 40 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS E 40 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS E 40 " 0.220 2.00e-02 2.50e+03 pdb=" HD2 HIS E 40 " 0.075 2.00e-02 2.50e+03 pdb=" HE1 HIS E 40 " -0.079 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1403 2.18 - 2.78: 41478 2.78 - 3.39: 59201 3.39 - 3.99: 74874 3.99 - 4.60: 114212 Nonbonded interactions: 291168 Sorted by model distance: nonbonded pdb=" OG SER E 100 " pdb=" H THR E 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER F 100 " pdb=" H THR F 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER B 100 " pdb=" H THR B 101 " model vdw 1.575 1.850 nonbonded pdb=" OG SER A 100 " pdb=" H THR A 101 " model vdw 1.576 1.850 nonbonded pdb=" OG SER D 100 " pdb=" H THR D 101 " model vdw 1.576 1.850 ... (remaining 291163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 6762 2.51 5 N 1890 2.21 5 O 2004 1.98 5 H 10752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.350 Extract box with map and model: 5.710 Check model and map are aligned: 0.340 Process input model: 69.410 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.023 0.138 10950 Z= 1.466 Angle : 1.427 10.186 14802 Z= 1.014 Chirality : 0.115 0.367 1596 Planarity : 0.012 0.053 1932 Dihedral : 9.581 73.959 4176 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.88 % Allowed : 2.65 % Favored : 96.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.57 (0.20), residues: 1356 helix: -0.10 (0.15), residues: 942 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.5704 time to fit residues: 363.2950 Evaluate side-chains 336 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B 225 GLN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN E 91 GLN ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10950 Z= 0.213 Angle : 0.594 4.298 14802 Z= 0.327 Chirality : 0.039 0.138 1596 Planarity : 0.006 0.051 1932 Dihedral : 4.153 22.615 1470 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.95 % Favored : 96.61 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.88 (0.21), residues: 1356 helix: 1.12 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.51 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 323 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 330 average time/residue: 0.4296 time to fit residues: 205.9795 Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 292 time to evaluate : 1.640 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2671 time to fit residues: 7.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 0.0270 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN E 25 ASN F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10950 Z= 0.167 Angle : 0.522 4.323 14802 Z= 0.282 Chirality : 0.038 0.135 1596 Planarity : 0.004 0.035 1932 Dihedral : 3.924 21.213 1470 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.38 (0.22), residues: 1356 helix: 1.54 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.43 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 303 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 308 average time/residue: 0.4287 time to fit residues: 193.5949 Evaluate side-chains 307 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 296 time to evaluate : 1.726 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2411 time to fit residues: 7.1891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS E 180 ASN F 38 HIS F 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 10950 Z= 0.150 Angle : 0.494 5.668 14802 Z= 0.260 Chirality : 0.037 0.132 1596 Planarity : 0.004 0.035 1932 Dihedral : 3.790 21.198 1470 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.73 (0.22), residues: 1356 helix: 1.85 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 306 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 307 average time/residue: 0.4322 time to fit residues: 198.7358 Evaluate side-chains 307 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 300 time to evaluate : 1.902 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2418 time to fit residues: 5.7795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 25 ASN B 38 HIS ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS E 25 ASN E 38 HIS F 38 HIS F 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10950 Z= 0.137 Angle : 0.481 4.182 14802 Z= 0.252 Chirality : 0.037 0.130 1596 Planarity : 0.003 0.036 1932 Dihedral : 3.683 20.668 1470 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.99 (0.22), residues: 1356 helix: 2.04 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.26 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 305 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 305 average time/residue: 0.4193 time to fit residues: 186.3914 Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 295 time to evaluate : 1.648 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2131 time to fit residues: 5.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 38 HIS E 38 HIS F 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10950 Z= 0.220 Angle : 0.510 4.144 14802 Z= 0.273 Chirality : 0.038 0.127 1596 Planarity : 0.004 0.037 1932 Dihedral : 3.678 19.886 1470 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.97 (0.22), residues: 1356 helix: 2.00 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.24 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 313 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 316 average time/residue: 0.4122 time to fit residues: 193.3041 Evaluate side-chains 319 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 310 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2277 time to fit residues: 6.2520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS C 38 HIS E 38 HIS F 21 GLN F 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10950 Z= 0.148 Angle : 0.477 4.076 14802 Z= 0.249 Chirality : 0.037 0.141 1596 Planarity : 0.003 0.061 1932 Dihedral : 3.634 21.177 1470 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.23 (0.23), residues: 1356 helix: 2.19 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 307 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 311 average time/residue: 0.4420 time to fit residues: 199.5799 Evaluate side-chains 309 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 1.695 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2516 time to fit residues: 5.8844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN D 25 ASN F 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10950 Z= 0.209 Angle : 0.503 4.133 14802 Z= 0.267 Chirality : 0.038 0.128 1596 Planarity : 0.004 0.050 1932 Dihedral : 3.637 20.389 1470 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.17 (0.23), residues: 1356 helix: 2.11 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -0.08 (0.29), residues: 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 311 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 311 average time/residue: 0.4327 time to fit residues: 195.3711 Evaluate side-chains 312 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 307 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2238 time to fit residues: 4.3853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS D 25 ASN E 180 ASN F 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10950 Z= 0.170 Angle : 0.491 4.637 14802 Z= 0.259 Chirality : 0.038 0.128 1596 Planarity : 0.003 0.053 1932 Dihedral : 3.637 20.971 1470 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.22 (0.23), residues: 1356 helix: 2.14 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 298 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 298 average time/residue: 0.4221 time to fit residues: 185.0203 Evaluate side-chains 300 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 296 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2144 time to fit residues: 4.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN F 38 HIS F 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 10950 Z= 0.161 Angle : 0.483 6.745 14802 Z= 0.253 Chirality : 0.037 0.139 1596 Planarity : 0.004 0.087 1932 Dihedral : 3.598 19.461 1470 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.29 (0.23), residues: 1356 helix: 2.19 (0.17), residues: 942 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 295 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 295 average time/residue: 0.3989 time to fit residues: 176.2994 Evaluate side-chains 300 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2441 time to fit residues: 5.0852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128032 restraints weight = 41942.149| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.13 r_work: 0.3487 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10950 Z= 0.164 Angle : 0.481 6.457 14802 Z= 0.252 Chirality : 0.037 0.131 1596 Planarity : 0.004 0.108 1932 Dihedral : 3.574 18.698 1470 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.36 (0.23), residues: 1356 helix: 2.25 (0.17), residues: 942 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 414 =============================================================================== Job complete usr+sys time: 5224.68 seconds wall clock time: 92 minutes 43.28 seconds (5563.28 seconds total)