Starting phenix.real_space_refine on Sat May 2 14:15:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.map" model { file = "/net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qqf_53300/05_2026/9qqf_53300.cif" } resolution = 3.23 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= 0.032 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 3902 2.51 5 N 1074 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6207 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1434 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1672 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2244 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 14, 'TRANS': 260} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 812 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Time building chain proxies: 1.22, per 1000 atoms: 0.20 Number of scatterers: 6207 At special positions: 0 Unit cell: (70.731, 74.796, 145.527, 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 1209 8.00 N 1074 7.00 C 3902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.02 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 100 " distance=2.03 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: 0.41 Conformation dependent library (CDL) restraints added in 299.0 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 21 sheets defined 12.6% alpha, 45.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.535A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.599A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 188 through 195 removed outlier: 3.585A pdb=" N TYR L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.625A pdb=" N GLU A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 54' Processing helix chain 'A' and resid 56 through 86 removed outlier: 3.747A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.617A pdb=" N THR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.504A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.994A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.685A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.559A pdb=" N SER H 109 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.507A pdb=" N PHE H 129 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 145 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.507A pdb=" N PHE H 129 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 145 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.611A pdb=" N ASP L 76 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR L 103 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.631A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.656A pdb=" N ASN L 144 " --> pdb=" O TYR L 179 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.738A pdb=" N CYS L 200 " --> pdb=" O LYS L 213 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS L 213 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 211 " --> pdb=" O VAL L 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.081A pdb=" N ILE A 95 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.081A pdb=" N ILE A 95 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 98 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AB7, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.694A pdb=" N ALA A 245 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.694A pdb=" N ALA A 245 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AC1, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.446A pdb=" N CYS A 259 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 272 " --> pdb=" O CYS A 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 31 removed outlier: 5.870A pdb=" N TYR B 46 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR B 86 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER B 48 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 84 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 50 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.767A pdb=" N GLU B 56 " --> pdb=" O ASN B 103 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1323 1.32 - 1.44: 1699 1.44 - 1.57: 3311 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6363 Sorted by residual: bond pdb=" CA GLN L 44 " pdb=" C GLN L 44 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.29e-02 6.01e+03 2.53e+01 bond pdb=" CA PHE B 82 " pdb=" C PHE B 82 " ideal model delta sigma weight residual 1.526 1.463 0.064 1.37e-02 5.33e+03 2.16e+01 bond pdb=" CA TYR L 42 " pdb=" C TYR L 42 " ideal model delta sigma weight residual 1.521 1.464 0.057 1.24e-02 6.50e+03 2.10e+01 bond pdb=" CA LYS L 45 " pdb=" C LYS L 45 " ideal model delta sigma weight residual 1.528 1.479 0.048 1.08e-02 8.57e+03 1.98e+01 bond pdb=" CA TRP L 41 " pdb=" C TRP L 41 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.19e-02 7.06e+03 1.83e+01 ... (remaining 6358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 8102 2.85 - 5.70: 427 5.70 - 8.55: 76 8.55 - 11.40: 31 11.40 - 14.25: 10 Bond angle restraints: 8646 Sorted by residual: angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" C GLY H 10 " ideal model delta sigma weight residual 112.49 124.62 -12.13 1.21e+00 6.83e-01 1.01e+02 angle pdb=" N LYS L 196 " pdb=" CA LYS L 196 " pdb=" C LYS L 196 " ideal model delta sigma weight residual 111.36 122.12 -10.76 1.09e+00 8.42e-01 9.74e+01 angle pdb=" N ASP L 9 " pdb=" CA ASP L 9 " pdb=" C ASP L 9 " ideal model delta sigma weight residual 111.69 100.36 11.33 1.23e+00 6.61e-01 8.48e+01 angle pdb=" C HIS B 51 " pdb=" N PRO B 52 " pdb=" CA PRO B 52 " ideal model delta sigma weight residual 119.82 111.44 8.38 9.80e-01 1.04e+00 7.32e+01 angle pdb=" N ALA A 41 " pdb=" CA ALA A 41 " pdb=" C ALA A 41 " ideal model delta sigma weight residual 111.28 120.58 -9.30 1.09e+00 8.42e-01 7.28e+01 ... (remaining 8641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 3343 16.24 - 32.48: 337 32.48 - 48.72: 78 48.72 - 64.95: 21 64.95 - 81.19: 5 Dihedral angle restraints: 3784 sinusoidal: 1495 harmonic: 2289 Sorted by residual: dihedral pdb=" C TRP B 80 " pdb=" N TRP B 80 " pdb=" CA TRP B 80 " pdb=" CB TRP B 80 " ideal model delta harmonic sigma weight residual -122.60 -136.05 13.45 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" N HIS B 51 " pdb=" C HIS B 51 " pdb=" CA HIS B 51 " pdb=" CB HIS B 51 " ideal model delta harmonic sigma weight residual 122.80 136.09 -13.29 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" C HIS B 51 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " pdb=" CB HIS B 51 " ideal model delta harmonic sigma weight residual -122.60 -135.17 12.57 0 2.50e+00 1.60e-01 2.53e+01 ... (remaining 3781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 818 0.142 - 0.284: 89 0.284 - 0.427: 8 0.427 - 0.569: 8 0.569 - 0.711: 1 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA HIS B 51 " pdb=" N HIS B 51 " pdb=" C HIS B 51 " pdb=" CB HIS B 51 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA TRP B 80 " pdb=" N TRP B 80 " pdb=" C TRP B 80 " pdb=" CB TRP B 80 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ASP L 88 " pdb=" N ASP L 88 " pdb=" C ASP L 88 " pdb=" CB ASP L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 ... (remaining 921 not shown) Planarity restraints: 1124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 155 " -0.049 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO H 156 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO L 8 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 146 " -0.036 2.00e-02 2.50e+03 1.89e-02 7.13e+00 pdb=" CG TYR L 146 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR L 146 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR L 146 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR L 146 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 146 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR L 146 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 146 " -0.011 2.00e-02 2.50e+03 ... (remaining 1121 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 233 2.67 - 3.23: 5928 3.23 - 3.78: 10191 3.78 - 4.34: 13460 4.34 - 4.90: 22256 Nonbonded interactions: 52068 Sorted by model distance: nonbonded pdb=" O ASP A 223 " pdb=" OD1 ASP A 223 " model vdw 2.112 3.040 nonbonded pdb=" O GLU H 42 " pdb=" OE1 GLU H 42 " model vdw 2.130 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.262 3.040 nonbonded pdb=" N GLN H 178 " pdb=" O LEU H 182 " model vdw 2.276 3.120 nonbonded pdb=" CD1 LEU B 84 " pdb=" CE1 TYR B 86 " model vdw 2.320 3.760 ... (remaining 52063 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.011 0.074 6369 Z= 0.814 Angle : 1.535 14.251 8658 Z= 0.990 Chirality : 0.100 0.711 924 Planarity : 0.007 0.075 1124 Dihedral : 14.060 81.193 2298 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 0.60 % Allowed : 16.69 % Favored : 82.71 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.26 (0.30), residues: 772 helix: 1.39 (0.56), residues: 86 sheet: -0.22 (0.28), residues: 340 loop : -0.38 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 87 TYR 0.036 0.003 TYR L 146 PHE 0.023 0.003 PHE B 50 TRP 0.018 0.002 TRP A 60 HIS 0.011 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.01110 ( 6363) covalent geometry : angle 1.53613 ( 8646) SS BOND : bond 0.00790 ( 6) SS BOND : angle 0.94295 ( 12) hydrogen bonds : bond 0.24124 ( 232) hydrogen bonds : angle 9.69115 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8320 (mmmm) REVERT: H 173 PHE cc_start: 0.8232 (m-80) cc_final: 0.7926 (m-80) REVERT: L 17 GLU cc_start: 0.8876 (mp0) cc_final: 0.7709 (mp0) REVERT: L 88 ASP cc_start: 0.8605 (m-30) cc_final: 0.8327 (m-30) REVERT: L 114 ARG cc_start: 0.8023 (ttt-90) cc_final: 0.7734 (ttt-90) REVERT: L 128 ASP cc_start: 0.7935 (p0) cc_final: 0.7510 (p0) REVERT: L 167 GLU cc_start: 0.8608 (pm20) cc_final: 0.8326 (pm20) outliers start: 4 outliers final: 2 residues processed: 124 average time/residue: 0.0930 time to fit residues: 14.5581 Evaluate side-chains 74 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN L 144 ASN ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.075406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062214 restraints weight = 26171.144| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.25 r_work: 0.3232 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6369 Z= 0.162 Angle : 0.673 7.282 8658 Z= 0.359 Chirality : 0.045 0.176 924 Planarity : 0.005 0.041 1124 Dihedral : 5.690 44.905 866 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 16.24 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.30), residues: 772 helix: 1.68 (0.57), residues: 82 sheet: -0.10 (0.28), residues: 345 loop : -0.46 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.024 0.002 TYR L 198 PHE 0.013 0.002 PHE A 208 TRP 0.019 0.001 TRP L 154 HIS 0.016 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6363) covalent geometry : angle 0.67303 ( 8646) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.62014 ( 12) hydrogen bonds : bond 0.04369 ( 232) hydrogen bonds : angle 6.71119 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8916 (tt0) cc_final: 0.8688 (tt0) REVERT: H 151 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: L 17 GLU cc_start: 0.8909 (mp0) cc_final: 0.7789 (mp0) REVERT: L 88 ASP cc_start: 0.8449 (m-30) cc_final: 0.8085 (m-30) REVERT: L 166 GLN cc_start: 0.7170 (tp40) cc_final: 0.6968 (tp-100) REVERT: A 98 MET cc_start: 0.8034 (tmm) cc_final: 0.7800 (tmm) REVERT: A 206 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (mt) REVERT: B 111 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8331 (mtmt) outliers start: 16 outliers final: 8 residues processed: 98 average time/residue: 0.0806 time to fit residues: 10.5041 Evaluate side-chains 74 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3604 r_free = 0.3604 target = 0.071756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058771 restraints weight = 26697.224| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.13 r_work: 0.3129 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6369 Z= 0.305 Angle : 0.724 8.917 8658 Z= 0.384 Chirality : 0.047 0.250 924 Planarity : 0.005 0.055 1124 Dihedral : 5.612 22.147 863 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.13 % Allowed : 16.84 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.48 (0.31), residues: 772 helix: 1.41 (0.57), residues: 81 sheet: -0.42 (0.28), residues: 349 loop : -0.47 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 114 TYR 0.018 0.002 TYR B 83 PHE 0.020 0.003 PHE H 107 TRP 0.014 0.002 TRP H 110 HIS 0.015 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 6363) covalent geometry : angle 0.72380 ( 8646) SS BOND : bond 0.00438 ( 6) SS BOND : angle 0.71485 ( 12) hydrogen bonds : bond 0.04618 ( 232) hydrogen bonds : angle 6.62576 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8418 (mmmm) REVERT: L 17 GLU cc_start: 0.8920 (mp0) cc_final: 0.7826 (mp0) REVERT: L 88 ASP cc_start: 0.8550 (m-30) cc_final: 0.8159 (m-30) REVERT: L 166 GLN cc_start: 0.7368 (tp40) cc_final: 0.7155 (tp-100) REVERT: L 169 VAL cc_start: 0.5611 (OUTLIER) cc_final: 0.5400 (p) REVERT: A 98 MET cc_start: 0.8088 (tmm) cc_final: 0.7791 (tmm) REVERT: B 111 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8522 (mtpt) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.0920 time to fit residues: 10.3785 Evaluate side-chains 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3647 r_free = 0.3647 target = 0.073296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.060151 restraints weight = 26262.937| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.23 r_work: 0.3181 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6369 Z= 0.161 Angle : 0.611 7.407 8658 Z= 0.323 Chirality : 0.044 0.185 924 Planarity : 0.004 0.045 1124 Dihedral : 5.253 21.696 863 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 17.44 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.38 (0.30), residues: 772 helix: 1.55 (0.58), residues: 81 sheet: -0.37 (0.29), residues: 333 loop : -0.42 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 114 TYR 0.018 0.002 TYR L 146 PHE 0.012 0.002 PHE H 107 TRP 0.012 0.001 TRP L 154 HIS 0.011 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6363) covalent geometry : angle 0.61101 ( 8646) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.51317 ( 12) hydrogen bonds : bond 0.03705 ( 232) hydrogen bonds : angle 5.95539 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8351 (mmmm) REVERT: H 157 VAL cc_start: 0.7118 (m) cc_final: 0.6797 (m) REVERT: L 17 GLU cc_start: 0.8808 (mp0) cc_final: 0.7795 (mp0) REVERT: L 88 ASP cc_start: 0.8365 (m-30) cc_final: 0.7978 (m-30) REVERT: L 166 GLN cc_start: 0.7410 (tp40) cc_final: 0.7149 (tp-100) REVERT: A 98 MET cc_start: 0.8087 (tmm) cc_final: 0.7815 (tmm) REVERT: B 111 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8533 (mtmt) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.0775 time to fit residues: 8.8448 Evaluate side-chains 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.0040 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.0010 chunk 44 optimal weight: 8.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3663 r_free = 0.3663 target = 0.073930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.060977 restraints weight = 26731.032| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.23 r_work: 0.3196 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6369 Z= 0.137 Angle : 0.596 8.466 8658 Z= 0.311 Chirality : 0.043 0.171 924 Planarity : 0.004 0.040 1124 Dihedral : 5.012 20.057 863 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.28 % Allowed : 18.18 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.35 (0.31), residues: 772 helix: 1.64 (0.57), residues: 81 sheet: -0.40 (0.29), residues: 336 loop : -0.36 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 114 TYR 0.016 0.001 TYR L 146 PHE 0.010 0.001 PHE H 107 TRP 0.010 0.001 TRP A 244 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6363) covalent geometry : angle 0.59629 ( 8646) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.45164 ( 12) hydrogen bonds : bond 0.03500 ( 232) hydrogen bonds : angle 5.62289 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8301 (mmmm) REVERT: L 17 GLU cc_start: 0.8840 (mp0) cc_final: 0.7815 (mp0) REVERT: L 88 ASP cc_start: 0.8309 (m-30) cc_final: 0.7935 (m-30) REVERT: L 166 GLN cc_start: 0.7469 (tp40) cc_final: 0.7154 (tp40) REVERT: A 98 MET cc_start: 0.8093 (tmm) cc_final: 0.7844 (tmm) REVERT: A 204 TRP cc_start: 0.8463 (m100) cc_final: 0.8093 (m100) REVERT: B 94 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8589 (mp0) REVERT: B 111 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8580 (mtmt) outliers start: 22 outliers final: 22 residues processed: 87 average time/residue: 0.0745 time to fit residues: 8.7599 Evaluate side-chains 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 104 HIS ** 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 = 0.3599 r_free = 0.3599 target = 0.071169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058514 restraints weight = 26935.179| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.04 r_work: 0.3132 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6369 Z= 0.289 Angle : 0.674 7.285 8658 Z= 0.356 Chirality : 0.045 0.197 924 Planarity : 0.005 0.043 1124 Dihedral : 5.369 19.091 863 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.02 % Allowed : 18.03 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.51 (0.31), residues: 772 helix: 0.81 (0.55), residues: 87 sheet: -0.38 (0.29), residues: 340 loop : -0.43 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.018 0.002 TYR B 83 PHE 0.020 0.002 PHE H 107 TRP 0.010 0.001 TRP A 244 HIS 0.014 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 6363) covalent geometry : angle 0.67389 ( 8646) SS BOND : bond 0.00454 ( 6) SS BOND : angle 0.61392 ( 12) hydrogen bonds : bond 0.04082 ( 232) hydrogen bonds : angle 6.00033 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8472 (mmmm) REVERT: L 17 GLU cc_start: 0.8791 (mp0) cc_final: 0.7730 (mp0) REVERT: L 88 ASP cc_start: 0.8461 (m-30) cc_final: 0.8050 (m-30) REVERT: L 166 GLN cc_start: 0.7475 (tp40) cc_final: 0.7175 (tp40) REVERT: L 167 GLU cc_start: 0.8595 (pm20) cc_final: 0.8365 (pm20) REVERT: L 169 VAL cc_start: 0.5677 (OUTLIER) cc_final: 0.5468 (p) REVERT: A 98 MET cc_start: 0.8177 (tmm) cc_final: 0.7891 (tmm) REVERT: B 94 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8566 (mp0) REVERT: B 111 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8553 (mtmt) outliers start: 27 outliers final: 23 residues processed: 82 average time/residue: 0.0823 time to fit residues: 8.9066 Evaluate side-chains 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3628 r_free = 0.3628 target = 0.072418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.059688 restraints weight = 26649.962| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.11 r_work: 0.3164 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6369 Z= 0.181 Angle : 0.633 8.388 8658 Z= 0.328 Chirality : 0.043 0.174 924 Planarity : 0.004 0.041 1124 Dihedral : 5.202 19.808 863 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.58 % Allowed : 18.93 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.54 (0.31), residues: 772 helix: 0.92 (0.56), residues: 87 sheet: -0.39 (0.30), residues: 333 loop : -0.51 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.017 0.002 TYR L 146 PHE 0.015 0.002 PHE H 68 TRP 0.009 0.001 TRP A 133 HIS 0.011 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6363) covalent geometry : angle 0.63287 ( 8646) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.51301 ( 12) hydrogen bonds : bond 0.03662 ( 232) hydrogen bonds : angle 5.71703 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8423 (mmmm) REVERT: L 17 GLU cc_start: 0.8786 (mp0) cc_final: 0.7716 (mp0) REVERT: L 88 ASP cc_start: 0.8430 (m-30) cc_final: 0.8008 (m-30) REVERT: L 166 GLN cc_start: 0.7523 (tp40) cc_final: 0.7203 (tp40) REVERT: L 167 GLU cc_start: 0.8588 (pm20) cc_final: 0.8375 (pm20) REVERT: A 21 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7216 (tpt170) REVERT: A 98 MET cc_start: 0.8141 (tmm) cc_final: 0.7877 (tmm) REVERT: A 204 TRP cc_start: 0.8547 (m100) cc_final: 0.8155 (m100) REVERT: B 111 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8492 (mtmt) outliers start: 24 outliers final: 22 residues processed: 83 average time/residue: 0.0912 time to fit residues: 9.9591 Evaluate side-chains 86 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 193 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3659 r_free = 0.3659 target = 0.074357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061616 restraints weight = 26847.112| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.14 r_work: 0.3193 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6369 Z= 0.123 Angle : 0.594 8.536 8658 Z= 0.307 Chirality : 0.042 0.156 924 Planarity : 0.004 0.040 1124 Dihedral : 4.942 20.242 863 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.58 % Allowed : 18.48 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.42 (0.31), residues: 772 helix: 1.12 (0.57), residues: 87 sheet: -0.36 (0.29), residues: 342 loop : -0.39 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.016 0.001 TYR L 146 PHE 0.017 0.001 PHE H 68 TRP 0.012 0.001 TRP A 204 HIS 0.008 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6363) covalent geometry : angle 0.59398 ( 8646) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.36488 ( 12) hydrogen bonds : bond 0.03356 ( 232) hydrogen bonds : angle 5.39027 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8291 (mmmm) REVERT: L 17 GLU cc_start: 0.8809 (mp0) cc_final: 0.7809 (mp0) REVERT: L 88 ASP cc_start: 0.8323 (m-30) cc_final: 0.7940 (m-30) REVERT: L 166 GLN cc_start: 0.7736 (tp40) cc_final: 0.7361 (tp40) REVERT: L 167 GLU cc_start: 0.8724 (pm20) cc_final: 0.8466 (pm20) REVERT: A 21 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7216 (tpt170) REVERT: A 98 MET cc_start: 0.8134 (tmm) cc_final: 0.7866 (tmm) REVERT: B 111 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8592 (mtmt) outliers start: 24 outliers final: 22 residues processed: 84 average time/residue: 0.0864 time to fit residues: 9.5573 Evaluate side-chains 91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3656 r_free = 0.3656 target = 0.074242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061585 restraints weight = 26967.590| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.06 r_work: 0.3196 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6369 Z= 0.132 Angle : 0.601 8.887 8658 Z= 0.311 Chirality : 0.042 0.152 924 Planarity : 0.004 0.037 1124 Dihedral : 4.862 20.500 863 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.43 % Allowed : 19.08 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.34 (0.31), residues: 772 helix: 1.22 (0.57), residues: 86 sheet: -0.26 (0.29), residues: 335 loop : -0.41 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.014 0.001 TYR L 146 PHE 0.014 0.001 PHE H 68 TRP 0.011 0.001 TRP A 244 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6363) covalent geometry : angle 0.60089 ( 8646) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.36430 ( 12) hydrogen bonds : bond 0.03319 ( 232) hydrogen bonds : angle 5.31597 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8324 (mmmm) REVERT: L 17 GLU cc_start: 0.8828 (mp0) cc_final: 0.7815 (mp0) REVERT: L 88 ASP cc_start: 0.8279 (m-30) cc_final: 0.7903 (m-30) REVERT: L 166 GLN cc_start: 0.7701 (tp40) cc_final: 0.7310 (tp40) REVERT: L 167 GLU cc_start: 0.8761 (pm20) cc_final: 0.8486 (pm20) REVERT: A 21 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7279 (tpt170) REVERT: A 98 MET cc_start: 0.8176 (tmm) cc_final: 0.7907 (tmm) REVERT: A 204 TRP cc_start: 0.8399 (m100) cc_final: 0.8004 (m100) REVERT: B 111 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8520 (mtpt) outliers start: 23 outliers final: 22 residues processed: 84 average time/residue: 0.0870 time to fit residues: 9.7462 Evaluate side-chains 90 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3655 r_free = 0.3655 target = 0.074195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061518 restraints weight = 26932.118| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.04 r_work: 0.3194 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6369 Z= 0.141 Angle : 0.600 8.737 8658 Z= 0.311 Chirality : 0.042 0.155 924 Planarity : 0.004 0.037 1124 Dihedral : 4.839 20.560 863 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.28 % Allowed : 19.23 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.25 (0.31), residues: 772 helix: 1.27 (0.57), residues: 86 sheet: -0.24 (0.30), residues: 335 loop : -0.31 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.014 0.001 TYR H 106 PHE 0.015 0.002 PHE H 68 TRP 0.011 0.001 TRP A 244 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6363) covalent geometry : angle 0.60073 ( 8646) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.38940 ( 12) hydrogen bonds : bond 0.03337 ( 232) hydrogen bonds : angle 5.27244 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8376 (mmmm) REVERT: L 17 GLU cc_start: 0.8832 (mp0) cc_final: 0.7824 (mp0) REVERT: L 88 ASP cc_start: 0.8324 (m-30) cc_final: 0.7899 (m-30) REVERT: L 166 GLN cc_start: 0.7689 (tp40) cc_final: 0.7298 (tp40) REVERT: L 167 GLU cc_start: 0.8776 (pm20) cc_final: 0.8503 (pm20) REVERT: A 21 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7355 (tpt170) REVERT: A 98 MET cc_start: 0.8179 (tmm) cc_final: 0.7911 (tmm) REVERT: A 204 TRP cc_start: 0.8413 (m100) cc_final: 0.8036 (m100) REVERT: B 111 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8519 (mtpt) outliers start: 22 outliers final: 21 residues processed: 83 average time/residue: 0.0799 time to fit residues: 8.8999 Evaluate side-chains 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 95 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 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 = 0.3662 r_free = 0.3662 target = 0.074275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061627 restraints weight = 26582.423| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.04 r_work: 0.3202 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6369 Z= 0.134 Angle : 0.604 8.549 8658 Z= 0.314 Chirality : 0.042 0.150 924 Planarity : 0.004 0.037 1124 Dihedral : 4.826 20.695 863 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.28 % Allowed : 19.37 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.31), residues: 772 helix: 1.29 (0.56), residues: 86 sheet: -0.22 (0.30), residues: 335 loop : -0.32 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.013 0.001 TYR L 146 PHE 0.014 0.002 PHE H 68 TRP 0.011 0.001 TRP A 244 HIS 0.008 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6363) covalent geometry : angle 0.60401 ( 8646) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.34999 ( 12) hydrogen bonds : bond 0.03305 ( 232) hydrogen bonds : angle 5.21361 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.47 seconds wall clock time: 26 minutes 16.70 seconds (1576.70 seconds total)