Starting phenix.real_space_refine on Sat Aug 3 03:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bei_44479/08_2024/9bei_44479.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4174 2.51 5 N 1133 2.21 5 O 1320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6649 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1456 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 5, 'TRANS': 179} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Time building chain proxies: 5.16, per 1000 atoms: 0.78 Number of scatterers: 6649 At special positions: 0 Unit cell: (68.952, 91.936, 152.048, 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 22 16.00 O 1320 8.00 N 1133 7.00 C 4174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.05 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 235 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 160 " - pdb=" SG CYS L 220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 15 sheets defined 18.6% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Processing helix chain 'A' and resid 74 through 101 Processing helix chain 'A' and resid 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.562A pdb=" N ALA A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.542A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'H' and resid 225 through 231 removed outlier: 3.686A pdb=" N THR H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 243 Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.046A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 154 Processing helix chain 'L' and resid 209 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210 removed outlier: 5.399A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 33 removed outlier: 4.089A pdb=" N GLN H 29 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER H 33 " --> pdb=" O SER H 47 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER H 47 " --> pdb=" O SER H 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.833A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.630A pdb=" N SER H 159 " --> pdb=" O LYS H 182 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS H 179 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER H 219 " --> pdb=" O CYS H 179 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL H 220 " --> pdb=" O HIS H 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.630A pdb=" N SER H 159 " --> pdb=" O LYS H 182 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS H 182 " --> pdb=" O LEU H 217 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU H 217 " --> pdb=" O LYS H 182 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR H 184 " --> pdb=" O TYR H 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 190 through 194 removed outlier: 3.839A pdb=" N ASN H 236 " --> pdb=" O SER H 192 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN H 194 " --> pdb=" O ILE H 234 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE H 234 " --> pdb=" O ASN H 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'K' and resid 59 through 60 removed outlier: 5.418A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET K 34 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 29 through 31 Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.269A pdb=" N LEU L 36 " --> pdb=" O GLU L 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.597A pdb=" N TYR L 74 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 123 " --> pdb=" O GLN L 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 140 through 141 removed outlier: 5.719A pdb=" N TYR L 199 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 171 through 174 removed outlier: 3.785A pdb=" N LYS L 171 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR L 223 " --> pdb=" O LYS L 171 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN L 173 " --> pdb=" O GLU L 221 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU L 221 " --> pdb=" O GLN L 173 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL L 231 " --> pdb=" O VAL L 222 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 774 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: 1.88 Time building geometry restraints manager: 3.05 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: 2177 1.34 - 1.46: 1660 1.46 - 1.58: 2919 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6788 Sorted by residual: bond pdb=" CA CYS A 64 " pdb=" CB CYS A 64 " ideal model delta sigma weight residual 1.531 1.556 -0.025 1.83e-02 2.99e+03 1.85e+00 bond pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C CYS A 64 " pdb=" N LYS A 65 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.41e-02 5.03e+03 1.43e+00 bond pdb=" CG MET A 52 " pdb=" SD MET A 52 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CG LYS L 64 " pdb=" CD LYS L 64 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 6783 not shown) Histogram of bond angle deviations from ideal: 93.69 - 101.75: 8 101.75 - 109.82: 907 109.82 - 117.89: 4147 117.89 - 125.95: 4048 125.95 - 134.02: 104 Bond angle restraints: 9214 Sorted by residual: angle pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 114.40 127.41 -13.01 2.30e+00 1.89e-01 3.20e+01 angle pdb=" CG MET A 52 " pdb=" SD MET A 52 " pdb=" CE MET A 52 " ideal model delta sigma weight residual 100.90 93.69 7.21 2.20e+00 2.07e-01 1.07e+01 angle pdb=" CB LYS L 64 " pdb=" CG LYS L 64 " pdb=" CD LYS L 64 " ideal model delta sigma weight residual 111.30 118.83 -7.53 2.30e+00 1.89e-01 1.07e+01 angle pdb=" N ALA L 109 " pdb=" CA ALA L 109 " pdb=" C ALA L 109 " ideal model delta sigma weight residual 107.93 113.29 -5.36 1.65e+00 3.67e-01 1.05e+01 angle pdb=" C GLY K 8 " pdb=" N GLY K 9 " pdb=" CA GLY K 9 " ideal model delta sigma weight residual 121.87 116.81 5.06 1.64e+00 3.72e-01 9.52e+00 ... (remaining 9209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 3651 17.16 - 34.32: 336 34.32 - 51.48: 55 51.48 - 68.64: 12 68.64 - 85.80: 13 Dihedral angle restraints: 4067 sinusoidal: 1565 harmonic: 2502 Sorted by residual: dihedral pdb=" CA PHE H 185 " pdb=" C PHE H 185 " pdb=" N PRO H 186 " pdb=" CA PRO H 186 " ideal model delta harmonic sigma weight residual -180.00 -124.35 -55.65 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA TYR H 129 " pdb=" C TYR H 129 " pdb=" N ASN H 130 " pdb=" CA ASN H 130 " ideal model delta harmonic sigma weight residual 180.00 135.89 44.11 0 5.00e+00 4.00e-02 7.78e+01 dihedral pdb=" CA ALA L 109 " pdb=" C ALA L 109 " pdb=" N THR L 110 " pdb=" CA THR L 110 " ideal model delta harmonic sigma weight residual 180.00 137.29 42.71 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 868 0.061 - 0.121: 141 0.121 - 0.182: 13 0.182 - 0.242: 1 0.242 - 0.303: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLN L 225 " pdb=" N GLN L 225 " pdb=" C GLN L 225 " pdb=" CB GLN L 225 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA CYS A 54 " pdb=" N CYS A 54 " pdb=" C CYS A 54 " pdb=" CB CYS A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 1021 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 185 " 0.086 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO H 186 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO H 186 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO H 186 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 185 " 0.012 2.00e-02 2.50e+03 1.53e-02 4.10e+00 pdb=" CG PHE H 185 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE H 185 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE H 185 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE H 185 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 185 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 185 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C VAL B 272 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL B 272 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 273 " 0.010 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 108 2.59 - 3.17: 6061 3.17 - 3.75: 11137 3.75 - 4.32: 14400 4.32 - 4.90: 22832 Nonbonded interactions: 54538 Sorted by model distance: nonbonded pdb=" ND2 ASN H 130 " pdb=" O TYR H 134 " model vdw 2.016 3.120 nonbonded pdb=" OG1 THR H 174 " pdb=" OG1 THR H 222 " model vdw 2.200 3.040 nonbonded pdb=" O ALA B 214 " pdb=" OG SER B 217 " model vdw 2.216 3.040 nonbonded pdb=" O GLY A 49 " pdb=" OH TYR A 67 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 45 " pdb=" O VAL A 56 " model vdw 2.257 3.040 ... (remaining 54533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6788 Z= 0.209 Angle : 0.782 13.013 9214 Z= 0.425 Chirality : 0.046 0.303 1024 Planarity : 0.006 0.131 1188 Dihedral : 14.426 85.803 2447 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.93 (0.28), residues: 852 helix: 1.66 (0.42), residues: 152 sheet: -0.98 (0.30), residues: 293 loop : -2.75 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 51 HIS 0.003 0.001 HIS L 224 PHE 0.035 0.002 PHE H 185 TYR 0.025 0.002 TYR A 67 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.760 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: A 77 LEU cc_start: 0.7921 (mm) cc_final: 0.7393 (tp) REVERT: B 298 LEU cc_start: 0.8955 (tp) cc_final: 0.8117 (tp) REVERT: L 112 TYR cc_start: 0.7623 (m-80) cc_final: 0.7209 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2357 time to fit residues: 19.1358 Evaluate side-chains 48 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6788 Z= 0.210 Angle : 0.665 8.650 9214 Z= 0.348 Chirality : 0.045 0.245 1024 Planarity : 0.006 0.117 1188 Dihedral : 6.657 56.983 944 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.78 (0.28), residues: 852 helix: 1.76 (0.42), residues: 152 sheet: -0.87 (0.28), residues: 309 loop : -2.72 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 62 HIS 0.004 0.001 HIS B 285 PHE 0.012 0.002 PHE H 185 TYR 0.019 0.002 TYR H 136 ARG 0.006 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7832 (mm) cc_final: 0.7405 (tp) REVERT: B 298 LEU cc_start: 0.9008 (tp) cc_final: 0.8101 (tp) REVERT: L 112 TYR cc_start: 0.7676 (m-80) cc_final: 0.7264 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2091 time to fit residues: 17.4401 Evaluate side-chains 49 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6788 Z= 0.173 Angle : 0.636 8.164 9214 Z= 0.329 Chirality : 0.044 0.233 1024 Planarity : 0.005 0.111 1188 Dihedral : 6.254 53.197 944 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.61 (0.28), residues: 852 helix: 1.92 (0.42), residues: 152 sheet: -0.85 (0.28), residues: 328 loop : -2.60 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 73 HIS 0.004 0.001 HIS B 285 PHE 0.010 0.001 PHE B 268 TYR 0.012 0.001 TYR K 95 ARG 0.004 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7856 (mm) cc_final: 0.7428 (tp) REVERT: B 298 LEU cc_start: 0.8983 (tp) cc_final: 0.8232 (tp) REVERT: K 76 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7883 (mmmt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.2243 time to fit residues: 17.9071 Evaluate side-chains 49 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6788 Z= 0.221 Angle : 0.673 9.457 9214 Z= 0.346 Chirality : 0.045 0.253 1024 Planarity : 0.006 0.129 1188 Dihedral : 6.462 55.532 944 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.66 (0.28), residues: 852 helix: 1.80 (0.42), residues: 152 sheet: -0.99 (0.27), residues: 349 loop : -2.54 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 73 HIS 0.004 0.001 HIS B 285 PHE 0.043 0.002 PHE H 185 TYR 0.014 0.001 TYR B 306 ARG 0.005 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.9002 (tp) cc_final: 0.8225 (tp) REVERT: K 76 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7882 (mmmt) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.2075 time to fit residues: 16.1984 Evaluate side-chains 46 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN H 130 ASN ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 GLN ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6788 Z= 0.335 Angle : 0.776 8.998 9214 Z= 0.404 Chirality : 0.048 0.276 1024 Planarity : 0.006 0.126 1188 Dihedral : 7.190 59.857 944 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.98 % Favored : 89.91 % Rotamer: Outliers : 0.28 % Allowed : 5.10 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.93 (0.28), residues: 852 helix: 1.42 (0.41), residues: 152 sheet: -1.07 (0.27), residues: 329 loop : -2.67 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 73 HIS 0.006 0.002 HIS B 285 PHE 0.021 0.002 PHE L 144 TYR 0.024 0.002 TYR B 306 ARG 0.008 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.9151 (tp) cc_final: 0.8275 (tp) REVERT: K 34 MET cc_start: 0.7699 (mmp) cc_final: 0.7385 (mmm) REVERT: K 76 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7933 (mmmt) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1997 time to fit residues: 14.5524 Evaluate side-chains 46 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 GLN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6788 Z= 0.274 Angle : 0.733 9.525 9214 Z= 0.380 Chirality : 0.047 0.271 1024 Planarity : 0.006 0.124 1188 Dihedral : 7.041 57.764 944 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.98 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.90 (0.28), residues: 852 helix: 1.51 (0.41), residues: 152 sheet: -1.16 (0.27), residues: 329 loop : -2.55 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 60 HIS 0.005 0.002 HIS B 285 PHE 0.021 0.002 PHE L 144 TYR 0.016 0.002 TYR B 296 ARG 0.007 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.9083 (tp) cc_final: 0.8167 (tp) REVERT: K 34 MET cc_start: 0.7557 (mmp) cc_final: 0.7301 (mmm) REVERT: K 76 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7934 (mmmt) REVERT: L 112 TYR cc_start: 0.7804 (m-80) cc_final: 0.7427 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1962 time to fit residues: 14.7969 Evaluate side-chains 45 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 0.0050 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6788 Z= 0.198 Angle : 0.696 9.771 9214 Z= 0.357 Chirality : 0.046 0.288 1024 Planarity : 0.006 0.118 1188 Dihedral : 6.703 55.787 944 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.39 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % 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: -1.77 (0.28), residues: 852 helix: 1.64 (0.41), residues: 152 sheet: -1.08 (0.28), residues: 314 loop : -2.45 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 60 HIS 0.007 0.001 HIS B 241 PHE 0.016 0.001 PHE L 144 TYR 0.011 0.001 TYR B 306 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.8985 (tp) cc_final: 0.8132 (tp) REVERT: K 76 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7917 (mmmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2100 time to fit residues: 16.5338 Evaluate side-chains 46 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6788 Z= 0.175 Angle : 0.682 9.433 9214 Z= 0.346 Chirality : 0.045 0.281 1024 Planarity : 0.005 0.116 1188 Dihedral : 6.344 52.797 944 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % 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: -1.62 (0.28), residues: 852 helix: 1.78 (0.42), residues: 152 sheet: -0.93 (0.29), residues: 307 loop : -2.41 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 128 HIS 0.003 0.001 HIS B 285 PHE 0.011 0.001 PHE L 144 TYR 0.022 0.001 TYR H 136 ARG 0.005 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.8941 (tp) cc_final: 0.8179 (tp) REVERT: K 29 ILE cc_start: 0.9199 (mm) cc_final: 0.8988 (mm) REVERT: K 76 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7952 (mmmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2280 time to fit residues: 17.4545 Evaluate side-chains 47 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6788 Z= 0.171 Angle : 0.695 10.487 9214 Z= 0.352 Chirality : 0.045 0.272 1024 Planarity : 0.005 0.129 1188 Dihedral : 6.303 57.784 944 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % 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: -1.56 (0.28), residues: 852 helix: 1.74 (0.42), residues: 152 sheet: -0.74 (0.29), residues: 303 loop : -2.45 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 128 HIS 0.003 0.001 HIS B 285 PHE 0.066 0.002 PHE H 185 TYR 0.012 0.001 TYR H 136 ARG 0.014 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.8937 (tp) cc_final: 0.8251 (tp) REVERT: K 29 ILE cc_start: 0.9212 (mm) cc_final: 0.9004 (mm) REVERT: K 76 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7949 (mmmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2107 time to fit residues: 16.4638 Evaluate side-chains 46 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.0170 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6788 Z= 0.172 Angle : 0.691 10.221 9214 Z= 0.347 Chirality : 0.045 0.316 1024 Planarity : 0.005 0.124 1188 Dihedral : 6.207 58.282 944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % 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: -1.48 (0.28), residues: 852 helix: 2.00 (0.42), residues: 145 sheet: -0.75 (0.28), residues: 317 loop : -2.40 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 128 HIS 0.007 0.001 HIS H 133 PHE 0.062 0.002 PHE H 185 TYR 0.012 0.001 TYR H 136 ARG 0.005 0.000 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 PHE cc_start: 0.8796 (t80) cc_final: 0.8512 (t80) REVERT: B 298 LEU cc_start: 0.8918 (tp) cc_final: 0.8253 (tp) REVERT: K 29 ILE cc_start: 0.9221 (mm) cc_final: 0.9016 (mm) REVERT: K 76 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7943 (mmmt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2096 time to fit residues: 16.8660 Evaluate side-chains 47 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.0370 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 225 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.092215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.069422 restraints weight = 47807.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069734 restraints weight = 34083.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.070377 restraints weight = 26202.420| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6788 Z= 0.237 Angle : 0.725 10.145 9214 Z= 0.367 Chirality : 0.047 0.306 1024 Planarity : 0.006 0.134 1188 Dihedral : 6.574 61.152 944 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.27 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % 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: -1.65 (0.28), residues: 852 helix: 1.65 (0.41), residues: 151 sheet: -0.90 (0.28), residues: 316 loop : -2.43 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 60 HIS 0.006 0.002 HIS H 133 PHE 0.050 0.002 PHE H 185 TYR 0.017 0.002 TYR L 80 ARG 0.005 0.001 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.71 seconds wall clock time: 29 minutes 41.53 seconds (1781.53 seconds total)