Starting phenix.real_space_refine (version: dev) on Mon Dec 12 08:21:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/12_2022/7s82_24889.pdb" } resolution = 3.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4806 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 4904 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2368 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2368 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 3.29, per 1000 atoms: 0.67 Number of scatterers: 4904 At special positions: 0 Unit cell: (73.789, 88.808, 73.789, 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 44 16.00 O 920 8.00 N 836 7.00 C 3104 6.00 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: 2.13 Conformation dependent library (CDL) restraints added in 698.3 milliseconds 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 28.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 4.306A pdb=" N GLY A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.725A pdb=" N ILE A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.239A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.113A pdb=" N GLY B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.698A pdb=" N MET B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.780A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.165A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 25 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.192A pdb=" N GLY A 79 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.616A pdb=" N TYR A 126 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 removed outlier: 7.006A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.256A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 38 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.256A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 5.681A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.853A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 462 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: 1.34 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1603 1.34 - 1.45: 759 1.45 - 1.57: 2582 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 5010 Sorted by residual: bond pdb=" CA MET B 82 " pdb=" C MET B 82 " ideal model delta sigma weight residual 1.533 1.513 0.020 9.60e-03 1.09e+04 4.17e+00 bond pdb=" CB THR A 175 " pdb=" CG2 THR A 175 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CG MET B 264 " pdb=" SD MET B 264 " ideal model delta sigma weight residual 1.803 1.768 0.035 2.50e-02 1.60e+03 1.94e+00 bond pdb=" C PRO A 122 " pdb=" N SER A 123 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.73e-02 3.34e+03 1.90e+00 bond pdb=" CG LEU B 87 " pdb=" CD1 LEU B 87 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 ... (remaining 5005 not shown) Histogram of bond angle deviations from ideal: 94.43 - 102.34: 24 102.34 - 110.25: 1094 110.25 - 118.15: 2703 118.15 - 126.06: 2913 126.06 - 133.97: 66 Bond angle restraints: 6800 Sorted by residual: angle pdb=" CA MET B 6 " pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CG MET B 264 " pdb=" SD MET B 264 " pdb=" CE MET B 264 " ideal model delta sigma weight residual 100.90 94.43 6.47 2.20e+00 2.07e-01 8.65e+00 angle pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" C ILE A 78 " ideal model delta sigma weight residual 111.88 108.85 3.03 1.06e+00 8.90e-01 8.20e+00 angle pdb=" CA GLN B 83 " pdb=" CB GLN B 83 " pdb=" CG GLN B 83 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.00e+00 angle pdb=" N GLN B 83 " pdb=" CA GLN B 83 " pdb=" C GLN B 83 " ideal model delta sigma weight residual 110.36 106.14 4.22 1.55e+00 4.16e-01 7.40e+00 ... (remaining 6795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2694 17.98 - 35.95: 223 35.95 - 53.93: 30 53.93 - 71.90: 4 71.90 - 89.88: 3 Dihedral angle restraints: 2954 sinusoidal: 1142 harmonic: 1812 Sorted by residual: dihedral pdb=" CA GLN B 83 " pdb=" C GLN B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR A 175 " pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PRO A 9 " pdb=" C PRO A 9 " pdb=" N SER A 10 " pdb=" CA SER A 10 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 380 0.027 - 0.053: 233 0.053 - 0.080: 92 0.080 - 0.106: 50 0.106 - 0.133: 11 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ASP B 155 " pdb=" N ASP B 155 " pdb=" C ASP B 155 " pdb=" CB ASP B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 763 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 209 " -0.015 2.00e-02 2.50e+03 1.81e-02 6.53e+00 pdb=" CG TYR B 209 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 209 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 209 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 209 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 209 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 209 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 209 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 251 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 252 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 52 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " 0.022 5.00e-02 4.00e+02 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 4905 3.22 - 3.78: 7818 3.78 - 4.34: 10519 4.34 - 4.90: 17589 Nonbonded interactions: 40952 Sorted by model distance: nonbonded pdb=" NE2 GLN B 83 " pdb=" O GLU B 178 " model vdw 2.097 2.520 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.179 2.440 nonbonded pdb=" OG SER A 145 " pdb=" O GLN C 0 " model vdw 2.187 2.440 nonbonded pdb=" NE2 GLN A 19 " pdb=" OD1 ASN A 119 " model vdw 2.205 2.520 nonbonded pdb=" OG1 THR A 224 " pdb=" OD1 ASP A 263 " model vdw 2.227 2.440 ... (remaining 40947 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 44 5.16 5 C 3104 2.51 5 N 836 2.21 5 O 920 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=0.69 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 2.850 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 17.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 5010 Z= 0.329 Angle : 0.720 7.342 6800 Z= 0.389 Chirality : 0.042 0.133 766 Planarity : 0.005 0.045 884 Dihedral : 13.223 89.878 1794 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % 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: -1.35 (0.34), residues: 626 helix: 0.93 (0.43), residues: 154 sheet: -3.05 (0.48), residues: 108 loop : -0.97 (0.32), residues: 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.612 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1420 time to fit residues: 25.2268 Evaluate side-chains 107 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 74 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** D 0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5010 Z= 0.219 Angle : 0.648 7.863 6800 Z= 0.330 Chirality : 0.041 0.147 766 Planarity : 0.005 0.052 884 Dihedral : 5.048 30.692 678 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.33), residues: 626 helix: 1.00 (0.41), residues: 152 sheet: -3.01 (0.50), residues: 88 loop : -1.16 (0.30), residues: 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.560 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 124 average time/residue: 0.1349 time to fit residues: 22.4794 Evaluate side-chains 113 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0486 time to fit residues: 0.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5010 Z= 0.191 Angle : 0.617 6.487 6800 Z= 0.312 Chirality : 0.041 0.149 766 Planarity : 0.004 0.046 884 Dihedral : 4.888 26.071 678 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.33), residues: 626 helix: 1.14 (0.42), residues: 152 sheet: -2.82 (0.52), residues: 88 loop : -1.14 (0.30), residues: 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.617 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.1315 time to fit residues: 22.9315 Evaluate side-chains 113 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 5010 Z= 0.284 Angle : 0.644 6.511 6800 Z= 0.319 Chirality : 0.042 0.161 766 Planarity : 0.004 0.048 884 Dihedral : 4.831 23.578 678 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.21 % 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: -1.15 (0.34), residues: 626 helix: 1.24 (0.43), residues: 152 sheet: -2.85 (0.54), residues: 88 loop : -1.07 (0.31), residues: 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.1363 time to fit residues: 22.1357 Evaluate side-chains 114 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0514 time to fit residues: 1.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5010 Z= 0.189 Angle : 0.624 7.411 6800 Z= 0.307 Chirality : 0.041 0.141 766 Planarity : 0.004 0.048 884 Dihedral : 4.717 22.674 678 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.65 % 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: -1.11 (0.33), residues: 626 helix: 1.29 (0.42), residues: 152 sheet: -2.76 (0.53), residues: 88 loop : -1.08 (0.30), residues: 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.530 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.1253 time to fit residues: 20.2812 Evaluate side-chains 112 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0506 time to fit residues: 1.2519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5010 Z= 0.194 Angle : 0.633 8.336 6800 Z= 0.308 Chirality : 0.042 0.185 766 Planarity : 0.004 0.049 884 Dihedral : 4.675 23.389 678 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.10 % 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: -1.01 (0.33), residues: 626 helix: 1.41 (0.43), residues: 152 sheet: -3.28 (0.56), residues: 64 loop : -1.07 (0.30), residues: 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.529 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 112 average time/residue: 0.1398 time to fit residues: 21.1198 Evaluate side-chains 102 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0480 time to fit residues: 1.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5010 Z= 0.202 Angle : 0.626 9.777 6800 Z= 0.304 Chirality : 0.041 0.137 766 Planarity : 0.004 0.049 884 Dihedral : 4.628 23.981 678 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.37 % 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: -1.08 (0.33), residues: 626 helix: 1.20 (0.41), residues: 154 sheet: -3.28 (0.50), residues: 84 loop : -0.89 (0.31), residues: 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1527 time to fit residues: 21.4457 Evaluate side-chains 100 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0531 time to fit residues: 0.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5010 Z= 0.243 Angle : 0.654 11.455 6800 Z= 0.319 Chirality : 0.042 0.189 766 Planarity : 0.004 0.051 884 Dihedral : 4.684 24.524 678 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.55 % 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: -1.08 (0.33), residues: 626 helix: 1.31 (0.42), residues: 152 sheet: -3.24 (0.56), residues: 74 loop : -1.04 (0.30), residues: 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.614 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.1466 time to fit residues: 21.0176 Evaluate side-chains 104 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0513 time to fit residues: 0.9071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5010 Z= 0.241 Angle : 0.658 9.790 6800 Z= 0.321 Chirality : 0.042 0.156 766 Planarity : 0.005 0.052 884 Dihedral : 4.718 24.931 678 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: -1.12 (0.33), residues: 626 helix: 1.25 (0.42), residues: 152 sheet: -3.26 (0.56), residues: 74 loop : -1.04 (0.30), residues: 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.614 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1358 time to fit residues: 19.5985 Evaluate side-chains 104 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5010 Z= 0.225 Angle : 0.653 10.474 6800 Z= 0.326 Chirality : 0.042 0.153 766 Planarity : 0.004 0.049 884 Dihedral : 4.706 25.126 678 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.55 % 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: -1.11 (0.33), residues: 626 helix: 1.15 (0.42), residues: 154 sheet: -3.20 (0.57), residues: 74 loop : -1.01 (0.31), residues: 398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.539 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.1299 time to fit residues: 18.7666 Evaluate side-chains 104 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0456 time to fit residues: 0.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113048 restraints weight = 8503.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117321 restraints weight = 4410.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120192 restraints weight = 2797.290| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5010 Z= 0.175 Angle : 0.611 9.555 6800 Z= 0.303 Chirality : 0.041 0.138 766 Planarity : 0.004 0.048 884 Dihedral : 4.582 23.703 678 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.37 % 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: -1.16 (0.34), residues: 626 helix: 1.14 (0.42), residues: 154 sheet: -3.25 (0.51), residues: 94 loop : -0.89 (0.31), residues: 378 =============================================================================== Job complete usr+sys time: 1276.26 seconds wall clock time: 24 minutes 6.37 seconds (1446.37 seconds total)