Starting phenix.real_space_refine on Wed Sep 17 07:40:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_44479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_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/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_44479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_44479.map" model { file = "/net/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_44479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bei_44479/09_2025/9bei_44479.cif" } resolution = 4.16 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 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.77, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 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: 0.61 Conformation dependent library (CDL) restraints added in 372.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.27 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: 1.19 Time building geometry restraints manager: 0.82 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: 0.00 - 2.60: 9077 2.60 - 5.21: 118 5.21 - 7.81: 17 7.81 - 10.41: 1 10.41 - 13.01: 1 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- 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 6794 Z= 0.162 Angle : 0.785 13.013 9226 Z= 0.427 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 : 21.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG B 208 TYR 0.025 0.002 TYR A 67 PHE 0.035 0.002 PHE H 185 TRP 0.018 0.002 TRP A 51 HIS 0.003 0.001 HIS L 224 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6788) covalent geometry : angle 0.78165 ( 9214) SS BOND : bond 0.00639 ( 6) SS BOND : angle 2.21915 ( 12) hydrogen bonds : bond 0.13694 ( 281) hydrogen bonds : angle 7.12199 ( 774) *********************** 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 to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.246 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: 0.1109 time to fit residues: 8.8335 Evaluate side-chains 48 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.093987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.069971 restraints weight = 48727.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.070883 restraints weight = 33130.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.071408 restraints weight = 26321.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.072032 restraints weight = 23257.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072405 restraints weight = 20991.276| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6794 Z= 0.135 Angle : 0.663 8.887 9226 Z= 0.346 Chirality : 0.045 0.243 1024 Planarity : 0.005 0.117 1188 Dihedral : 6.585 56.521 944 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.57 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.28), residues: 852 helix: 1.78 (0.42), residues: 152 sheet: -0.84 (0.28), residues: 311 loop : -2.71 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 208 TYR 0.019 0.001 TYR H 136 PHE 0.014 0.002 PHE H 185 TRP 0.008 0.001 TRP H 62 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6788) covalent geometry : angle 0.65946 ( 9214) SS BOND : bond 0.00593 ( 6) SS BOND : angle 1.89637 ( 12) hydrogen bonds : bond 0.03669 ( 281) hydrogen bonds : angle 5.98719 ( 774) *********************** 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 60 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7282 (mm) cc_final: 0.6880 (tp) REVERT: B 298 LEU cc_start: 0.9031 (tp) cc_final: 0.8088 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0829 time to fit residues: 6.6396 Evaluate side-chains 49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 0.0020 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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** ** 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 ** 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 = 0.4023 r_free = 0.4023 target = 0.093451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.069846 restraints weight = 47884.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.070950 restraints weight = 32384.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.071644 restraints weight = 25758.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.072259 restraints weight = 22226.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.072599 restraints weight = 20434.117| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6794 Z= 0.128 Angle : 0.640 7.932 9226 Z= 0.332 Chirality : 0.044 0.233 1024 Planarity : 0.005 0.111 1188 Dihedral : 6.312 53.784 944 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.14 % Allowed : 5.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.28), residues: 852 helix: 1.91 (0.42), residues: 152 sheet: -0.80 (0.28), residues: 314 loop : -2.59 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.011 0.001 TYR B 296 PHE 0.011 0.001 PHE L 108 TRP 0.006 0.001 TRP H 73 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6788) covalent geometry : angle 0.63755 ( 9214) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.76525 ( 12) hydrogen bonds : bond 0.03343 ( 281) hydrogen bonds : angle 5.74305 ( 774) *********************** 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 59 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7319 (mm) cc_final: 0.6919 (tp) REVERT: B 298 LEU cc_start: 0.9051 (tp) cc_final: 0.8241 (tp) REVERT: K 76 LYS cc_start: 0.8190 (mmpt) cc_final: 0.7883 (mmmt) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.0993 time to fit residues: 7.8524 Evaluate side-chains 49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 3 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.092997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070769 restraints weight = 48632.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.071124 restraints weight = 35507.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.071783 restraints weight = 26592.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072457 restraints weight = 22699.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.072786 restraints weight = 20129.585| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6794 Z= 0.143 Angle : 0.669 9.117 9226 Z= 0.344 Chirality : 0.045 0.262 1024 Planarity : 0.006 0.128 1188 Dihedral : 6.418 55.994 944 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.28), residues: 852 helix: 1.75 (0.42), residues: 152 sheet: -0.99 (0.27), residues: 349 loop : -2.55 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.015 0.001 TYR B 306 PHE 0.043 0.002 PHE H 185 TRP 0.018 0.001 TRP H 73 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6788) covalent geometry : angle 0.66567 ( 9214) SS BOND : bond 0.00674 ( 6) SS BOND : angle 1.83578 ( 12) hydrogen bonds : bond 0.03304 ( 281) hydrogen bonds : angle 5.78762 ( 774) *********************** 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 to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.249 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: 0.9113 (tp) cc_final: 0.8344 (tp) REVERT: K 76 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7861 (mmmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0964 time to fit residues: 7.5421 Evaluate side-chains 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.092087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.069069 restraints weight = 48857.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.069793 restraints weight = 33393.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070549 restraints weight = 26102.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.071211 restraints weight = 22328.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.071525 restraints weight = 20261.607| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6794 Z= 0.169 Angle : 0.696 8.701 9226 Z= 0.359 Chirality : 0.046 0.272 1024 Planarity : 0.006 0.125 1188 Dihedral : 6.581 55.915 944 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.39 % Favored : 90.49 % Rotamer: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.28), residues: 852 helix: 1.74 (0.41), residues: 152 sheet: -0.92 (0.27), residues: 335 loop : -2.62 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.020 0.002 TYR B 306 PHE 0.022 0.002 PHE H 185 TRP 0.012 0.001 TRP H 73 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6788) covalent geometry : angle 0.69318 ( 9214) SS BOND : bond 0.00766 ( 6) SS BOND : angle 1.85777 ( 12) hydrogen bonds : bond 0.03376 ( 281) hydrogen bonds : angle 5.77084 ( 774) *********************** 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 59 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.9086 (tp) cc_final: 0.8311 (tp) REVERT: K 76 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7887 (mmmt) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.0949 time to fit residues: 7.4553 Evaluate side-chains 47 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 130 ASN ** 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 215 HIS ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.089244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.065529 restraints weight = 50373.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066329 restraints weight = 34555.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067158 restraints weight = 26754.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067797 restraints weight = 23229.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.067980 restraints weight = 21359.219| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6794 Z= 0.292 Angle : 0.853 10.377 9226 Z= 0.445 Chirality : 0.050 0.292 1024 Planarity : 0.007 0.130 1188 Dihedral : 7.547 60.430 944 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.97 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.28), residues: 852 helix: 1.43 (0.41), residues: 152 sheet: -1.20 (0.28), residues: 318 loop : -2.66 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 31 TYR 0.023 0.003 TYR B 296 PHE 0.029 0.003 PHE L 144 TRP 0.013 0.002 TRP A 30 HIS 0.013 0.003 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 6788) covalent geometry : angle 0.84994 ( 9214) SS BOND : bond 0.00542 ( 6) SS BOND : angle 2.07590 ( 12) hydrogen bonds : bond 0.04335 ( 281) hydrogen bonds : angle 6.47088 ( 774) *********************** 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 51 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 34 MET cc_start: 0.7892 (mmp) cc_final: 0.7548 (mmm) REVERT: K 76 LYS cc_start: 0.8281 (mmpt) cc_final: 0.7973 (mmmt) REVERT: L 112 TYR cc_start: 0.7901 (m-80) cc_final: 0.7470 (m-80) REVERT: L 130 VAL cc_start: 0.8920 (p) cc_final: 0.8539 (p) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0987 time to fit residues: 6.7642 Evaluate side-chains 38 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 53 optimal weight: 0.3980 overall best weight: 1.4462 ------------------------------------------------------------------------------- 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** K 77 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.091740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.068600 restraints weight = 48178.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.069492 restraints weight = 33769.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.070024 restraints weight = 25697.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.070024 restraints weight = 22080.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.070024 restraints weight = 22080.925| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6794 Z= 0.159 Angle : 0.723 9.765 9226 Z= 0.371 Chirality : 0.046 0.288 1024 Planarity : 0.006 0.117 1188 Dihedral : 6.986 58.160 944 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.39 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.28), residues: 852 helix: 1.61 (0.41), residues: 152 sheet: -1.04 (0.28), residues: 312 loop : -2.62 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 208 TYR 0.013 0.002 TYR B 296 PHE 0.022 0.002 PHE L 144 TRP 0.046 0.002 TRP H 193 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6788) covalent geometry : angle 0.71973 ( 9214) SS BOND : bond 0.00583 ( 6) SS BOND : angle 2.01785 ( 12) hydrogen bonds : bond 0.03467 ( 281) hydrogen bonds : angle 6.05819 ( 774) *********************** 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 to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.270 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: 0.9105 (tp) cc_final: 0.8841 (tp) REVERT: K 34 MET cc_start: 0.7422 (mmp) cc_final: 0.7165 (mmm) REVERT: K 76 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7877 (mmmt) REVERT: L 112 TYR cc_start: 0.7852 (m-80) cc_final: 0.7385 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0942 time to fit residues: 7.3850 Evaluate side-chains 45 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 52 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.090718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.066750 restraints weight = 49191.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.067833 restraints weight = 34380.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.068340 restraints weight = 27463.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.068756 restraints weight = 23900.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.069146 restraints weight = 21936.986| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6794 Z= 0.195 Angle : 0.757 9.058 9226 Z= 0.390 Chirality : 0.048 0.283 1024 Planarity : 0.006 0.122 1188 Dihedral : 7.083 57.534 944 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.27 % Favored : 88.62 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.28), residues: 852 helix: 1.51 (0.41), residues: 152 sheet: -1.21 (0.28), residues: 326 loop : -2.67 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 208 TYR 0.018 0.002 TYR B 296 PHE 0.024 0.002 PHE L 144 TRP 0.029 0.002 TRP H 193 HIS 0.006 0.002 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6788) covalent geometry : angle 0.75394 ( 9214) SS BOND : bond 0.00649 ( 6) SS BOND : angle 1.96271 ( 12) hydrogen bonds : bond 0.03657 ( 281) hydrogen bonds : angle 6.14971 ( 774) *********************** 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 55 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.274 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: B 298 LEU cc_start: 0.9120 (tp) cc_final: 0.8852 (tp) REVERT: K 34 MET cc_start: 0.7547 (mmp) cc_final: 0.7267 (mmm) REVERT: K 76 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7994 (mmmt) REVERT: L 112 TYR cc_start: 0.7878 (m-80) cc_final: 0.7391 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0897 time to fit residues: 6.7734 Evaluate side-chains 45 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 57 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 269 ASN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.092372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.069579 restraints weight = 48990.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.070697 restraints weight = 32979.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.071386 restraints weight = 25780.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.071897 restraints weight = 22291.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.072328 restraints weight = 20498.868| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6794 Z= 0.130 Angle : 0.713 10.733 9226 Z= 0.362 Chirality : 0.046 0.294 1024 Planarity : 0.006 0.130 1188 Dihedral : 6.636 60.477 944 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.80 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.28), residues: 852 helix: 1.67 (0.42), residues: 152 sheet: -1.11 (0.28), residues: 314 loop : -2.55 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 93 TYR 0.018 0.001 TYR B 306 PHE 0.052 0.002 PHE H 185 TRP 0.024 0.002 TRP H 193 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6788) covalent geometry : angle 0.70914 ( 9214) SS BOND : bond 0.00368 ( 6) SS BOND : angle 2.04689 ( 12) hydrogen bonds : bond 0.03208 ( 281) hydrogen bonds : angle 5.81783 ( 774) *********************** 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 64 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8516 (pt0) REVERT: A 51 TRP cc_start: 0.7872 (t-100) cc_final: 0.7640 (m100) REVERT: A 77 LEU cc_start: 0.7964 (mm) cc_final: 0.7744 (mm) REVERT: B 298 LEU cc_start: 0.9071 (tp) cc_final: 0.8821 (tp) REVERT: K 76 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7949 (mmmt) REVERT: L 112 TYR cc_start: 0.7807 (m-80) cc_final: 0.7378 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1001 time to fit residues: 8.3907 Evaluate side-chains 51 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 25 optimal weight: 0.0030 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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 130 ASN H 210 GLN L 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.094668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.070417 restraints weight = 47470.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.071255 restraints weight = 33277.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.071956 restraints weight = 26449.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072361 restraints weight = 22617.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.072717 restraints weight = 20746.198| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6794 Z= 0.122 Angle : 0.710 10.182 9226 Z= 0.360 Chirality : 0.046 0.332 1024 Planarity : 0.005 0.125 1188 Dihedral : 6.308 58.843 944 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.57 % Favored : 91.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.28), residues: 852 helix: 1.79 (0.42), residues: 152 sheet: -0.91 (0.29), residues: 304 loop : -2.48 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 93 TYR 0.014 0.001 TYR B 306 PHE 0.060 0.002 PHE H 185 TRP 0.021 0.001 TRP H 193 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6788) covalent geometry : angle 0.70709 ( 9214) SS BOND : bond 0.00561 ( 6) SS BOND : angle 1.87029 ( 12) hydrogen bonds : bond 0.03068 ( 281) hydrogen bonds : angle 5.53371 ( 774) ********************** 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 64 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8554 (tt0) REVERT: A 27 LEU cc_start: 0.8964 (tt) cc_final: 0.8709 (tt) REVERT: A 77 LEU cc_start: 0.7733 (mm) cc_final: 0.7268 (tp) REVERT: B 268 PHE cc_start: 0.8681 (t80) cc_final: 0.8421 (t80) REVERT: B 298 LEU cc_start: 0.9071 (tp) cc_final: 0.8143 (tp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0987 time to fit residues: 8.3060 Evaluate side-chains 49 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 133 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 = 0.4053 r_free = 0.4053 target = 0.094667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.070797 restraints weight = 47822.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.071758 restraints weight = 33214.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.072422 restraints weight = 26034.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.072956 restraints weight = 22309.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.073240 restraints weight = 20409.122| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6794 Z= 0.121 Angle : 0.690 9.935 9226 Z= 0.349 Chirality : 0.045 0.330 1024 Planarity : 0.005 0.129 1188 Dihedral : 6.187 58.211 944 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.28), residues: 852 helix: 2.14 (0.42), residues: 146 sheet: -0.90 (0.28), residues: 318 loop : -2.39 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 93 TYR 0.016 0.001 TYR B 306 PHE 0.057 0.002 PHE H 185 TRP 0.019 0.001 TRP H 193 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6788) covalent geometry : angle 0.68763 ( 9214) SS BOND : bond 0.00589 ( 6) SS BOND : angle 1.74353 ( 12) hydrogen bonds : bond 0.03046 ( 281) hydrogen bonds : angle 5.44303 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.76 seconds wall clock time: 30 minutes 51.02 seconds (1851.02 seconds total)