Starting phenix.real_space_refine on Thu Jul 24 03:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.map" model { file = "/net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p74_17517/07_2025/8p74_17517.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 30 5.16 5 C 3267 2.51 5 N 864 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5115 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Unusual residues: {'ACE': 1} Classifications: {'peptide': 275, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'X3Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 5.87, per 1000 atoms: 1.15 Number of scatterers: 5115 At special positions: 0 Unit cell: (84.075, 94.05, 66.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 30 16.00 O 953 8.00 N 864 7.00 C 3267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.55 Conformation dependent library (CDL) restraints added in 2.0 seconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 62.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.649A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.821A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.924A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.621A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.670A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.520A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.156A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.316A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.619A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.683A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 20 removed outlier: 7.086A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 273 hydrogen bonds defined for protein. 762 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: 1.90 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 1663 1.37 - 1.51: 1490 1.51 - 1.65: 1992 1.65 - 1.80: 18 1.80 - 1.94: 30 Bond restraints: 5193 Sorted by residual: bond pdb=" C08 X3Z J 401 " pdb=" N09 X3Z J 401 " ideal model delta sigma weight residual 1.340 1.457 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C19 X3Z J 401 " pdb=" N20 X3Z J 401 " ideal model delta sigma weight residual 1.351 1.458 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C29 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.376 1.300 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N06 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.343 1.406 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" C16 X3Z J 401 " pdb="BR17 X3Z J 401 " ideal model delta sigma weight residual 1.896 1.938 -0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 5188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6849 1.57 - 3.14: 136 3.14 - 4.71: 34 4.71 - 6.29: 8 6.29 - 7.86: 2 Bond angle restraints: 7029 Sorted by residual: angle pdb=" N VAL J 210 " pdb=" CA VAL J 210 " pdb=" C VAL J 210 " ideal model delta sigma weight residual 109.19 106.12 3.07 8.20e-01 1.49e+00 1.40e+01 angle pdb=" C VAL J 210 " pdb=" CA VAL J 210 " pdb=" CB VAL J 210 " ideal model delta sigma weight residual 109.33 112.61 -3.28 9.80e-01 1.04e+00 1.12e+01 angle pdb=" CA VAL J 210 " pdb=" C VAL J 210 " pdb=" N PRO J 211 " ideal model delta sigma weight residual 116.57 119.74 -3.17 9.80e-01 1.04e+00 1.05e+01 angle pdb=" CB GLU I 49 " pdb=" CG GLU I 49 " pdb=" CD GLU I 49 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.70e+00 3.46e-01 6.54e+00 angle pdb=" CB ARG I 63 " pdb=" CG ARG I 63 " pdb=" CD ARG I 63 " ideal model delta sigma weight residual 111.30 116.79 -5.49 2.30e+00 1.89e-01 5.70e+00 ... (remaining 7024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2730 17.83 - 35.66: 294 35.66 - 53.49: 81 53.49 - 71.32: 24 71.32 - 89.15: 10 Dihedral angle restraints: 3139 sinusoidal: 1305 harmonic: 1834 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU H 262 " pdb=" CG GLU H 262 " pdb=" CD GLU H 262 " pdb=" OE1 GLU H 262 " ideal model delta sinusoidal sigma weight residual 0.00 89.15 -89.15 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU J 126 " pdb=" CG GLU J 126 " pdb=" CD GLU J 126 " pdb=" OE1 GLU J 126 " ideal model delta sinusoidal sigma weight residual 0.00 89.07 -89.07 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 460 0.029 - 0.058: 202 0.058 - 0.087: 71 0.087 - 0.117: 31 0.117 - 0.146: 8 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA VAL I 120 " pdb=" N VAL I 120 " pdb=" C VAL I 120 " pdb=" CB VAL I 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 769 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 231 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO J 232 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J 232 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 232 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO I 166 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO J 72 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.022 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 5269 3.28 - 3.82: 9404 3.82 - 4.36: 11233 4.36 - 4.90: 18312 Nonbonded interactions: 44578 Sorted by model distance: nonbonded pdb=" N GLU J 147 " pdb=" OE1 GLU J 147 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.208 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 502 " model vdw 2.228 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS I 114 " pdb=" O ILE J 55 " model vdw 2.297 3.120 ... (remaining 44573 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: 6.100 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 27.100 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:23.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.004 0.117 5193 Z= 0.201 Angle : 0.598 7.858 7029 Z= 0.301 Chirality : 0.041 0.146 772 Planarity : 0.005 0.044 897 Dihedral : 16.962 89.149 1951 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 0.91 % Allowed : 17.64 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.35), residues: 612 helix: 1.91 (0.29), residues: 332 sheet: -0.15 (0.94), residues: 29 loop : 0.50 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.12961 ( 273) hydrogen bonds : angle 5.64125 ( 762) covalent geometry : bond 0.00432 ( 5193) covalent geometry : angle 0.59797 ( 7029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.639 Fit side-chains REVERT: J 147 GLU cc_start: 0.7215 (pm20) cc_final: 0.6806 (pt0) outliers start: 5 outliers final: 5 residues processed: 93 average time/residue: 1.7013 time to fit residues: 164.0049 Evaluate side-chains 89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145890 restraints weight = 4943.187| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.10 r_work: 0.3635 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5193 Z= 0.130 Angle : 0.539 6.384 7029 Z= 0.277 Chirality : 0.041 0.155 772 Planarity : 0.005 0.040 897 Dihedral : 8.437 77.693 709 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 2.18 % Allowed : 14.73 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.35), residues: 612 helix: 2.04 (0.29), residues: 338 sheet: 1.01 (1.20), residues: 19 loop : 0.61 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 258 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 273) hydrogen bonds : angle 4.64155 ( 762) covalent geometry : bond 0.00291 ( 5193) covalent geometry : angle 0.53907 ( 7029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.622 Fit side-chains REVERT: J 99 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6598 (tt0) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 1.2837 time to fit residues: 128.3205 Evaluate side-chains 90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144338 restraints weight = 4610.095| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.03 r_work: 0.3614 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.192 Angle : 0.613 7.613 7029 Z= 0.312 Chirality : 0.044 0.154 772 Planarity : 0.006 0.044 897 Dihedral : 8.058 79.483 703 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.91 % Allowed : 14.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 612 helix: 1.73 (0.28), residues: 341 sheet: 0.88 (1.23), residues: 19 loop : 0.43 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.004 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 273) hydrogen bonds : angle 4.73214 ( 762) covalent geometry : bond 0.00442 ( 5193) covalent geometry : angle 0.61345 ( 7029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.622 Fit side-chains REVERT: H 249 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7112 (mt0) REVERT: J 11 ARG cc_start: 0.4882 (OUTLIER) cc_final: 0.4609 (tpt170) REVERT: J 99 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6608 (tt0) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 1.9073 time to fit residues: 188.9006 Evaluate side-chains 94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS J 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146297 restraints weight = 4751.876| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.06 r_work: 0.3641 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5193 Z= 0.125 Angle : 0.535 6.393 7029 Z= 0.273 Chirality : 0.041 0.148 772 Planarity : 0.005 0.041 897 Dihedral : 7.499 76.540 703 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 2.36 % Allowed : 15.09 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 612 helix: 2.01 (0.28), residues: 341 sheet: 0.73 (1.20), residues: 19 loop : 0.47 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS J 258 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 273) hydrogen bonds : angle 4.53519 ( 762) covalent geometry : bond 0.00278 ( 5193) covalent geometry : angle 0.53544 ( 7029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.883 Fit side-chains REVERT: J 14 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6931 (tttm) REVERT: J 99 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6588 (tt0) outliers start: 13 outliers final: 5 residues processed: 98 average time/residue: 2.0858 time to fit residues: 212.5763 Evaluate side-chains 91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 0.0050 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145942 restraints weight = 4717.928| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.05 r_work: 0.3635 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5193 Z= 0.132 Angle : 0.538 6.503 7029 Z= 0.274 Chirality : 0.041 0.152 772 Planarity : 0.005 0.040 897 Dihedral : 7.226 76.956 703 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.73 % Allowed : 15.09 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.34), residues: 612 helix: 2.04 (0.28), residues: 341 sheet: 0.47 (1.20), residues: 19 loop : 0.48 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 273) hydrogen bonds : angle 4.50189 ( 762) covalent geometry : bond 0.00298 ( 5193) covalent geometry : angle 0.53783 ( 7029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.639 Fit side-chains REVERT: H 249 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: I 261 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7392 (ptmm) REVERT: J 14 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6896 (tttm) REVERT: J 99 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6579 (tt0) outliers start: 15 outliers final: 6 residues processed: 95 average time/residue: 2.8483 time to fit residues: 283.3539 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144748 restraints weight = 4707.243| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.05 r_work: 0.3620 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5193 Z= 0.173 Angle : 0.595 7.759 7029 Z= 0.302 Chirality : 0.044 0.161 772 Planarity : 0.005 0.040 897 Dihedral : 7.298 78.603 703 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 14.73 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 612 helix: 1.80 (0.28), residues: 341 sheet: 0.55 (1.22), residues: 19 loop : 0.39 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.002 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 273) hydrogen bonds : angle 4.62675 ( 762) covalent geometry : bond 0.00395 ( 5193) covalent geometry : angle 0.59460 ( 7029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.941 Fit side-chains REVERT: I 242 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4471 (mmt180) REVERT: I 261 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7343 (ptmm) REVERT: J 14 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6837 (tttm) REVERT: J 99 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: J 293 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7780 (mptt) outliers start: 18 outliers final: 7 residues processed: 97 average time/residue: 1.7911 time to fit residues: 180.3190 Evaluate side-chains 97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.164700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145811 restraints weight = 4651.867| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.06 r_work: 0.3634 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5193 Z= 0.134 Angle : 0.550 6.982 7029 Z= 0.278 Chirality : 0.041 0.154 772 Planarity : 0.005 0.040 897 Dihedral : 7.049 76.861 703 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 2.73 % Allowed : 14.73 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.34), residues: 612 helix: 2.01 (0.28), residues: 341 sheet: 1.50 (1.49), residues: 9 loop : 0.38 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 273) hydrogen bonds : angle 4.51344 ( 762) covalent geometry : bond 0.00303 ( 5193) covalent geometry : angle 0.54956 ( 7029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.589 Fit side-chains REVERT: I 242 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.4577 (mmt180) REVERT: I 260 LYS cc_start: 0.7122 (tttm) cc_final: 0.6911 (ttpp) REVERT: I 261 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7334 (ptmm) REVERT: J 14 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6806 (tttm) REVERT: J 99 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: J 293 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7791 (mptt) outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 2.1498 time to fit residues: 214.4550 Evaluate side-chains 98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144983 restraints weight = 4706.737| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.07 r_work: 0.3622 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5193 Z= 0.158 Angle : 0.586 8.315 7029 Z= 0.298 Chirality : 0.043 0.168 772 Planarity : 0.005 0.040 897 Dihedral : 7.118 78.053 703 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.91 % Allowed : 14.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.34), residues: 612 helix: 1.90 (0.28), residues: 341 sheet: 0.51 (1.22), residues: 19 loop : 0.38 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.019 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 273) hydrogen bonds : angle 4.56939 ( 762) covalent geometry : bond 0.00360 ( 5193) covalent geometry : angle 0.58602 ( 7029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.731 Fit side-chains REVERT: H 249 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: I 242 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4550 (mmt180) REVERT: I 260 LYS cc_start: 0.7119 (tttm) cc_final: 0.6918 (ttpp) REVERT: I 261 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7338 (ptmm) REVERT: J 14 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6811 (tttm) REVERT: J 99 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: J 293 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7789 (mptt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 1.3760 time to fit residues: 134.3238 Evaluate side-chains 98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144125 restraints weight = 4703.192| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.06 r_work: 0.3612 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5193 Z= 0.195 Angle : 0.632 8.785 7029 Z= 0.321 Chirality : 0.045 0.156 772 Planarity : 0.006 0.040 897 Dihedral : 7.246 79.318 703 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 3.09 % Allowed : 14.00 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.34), residues: 612 helix: 1.69 (0.28), residues: 341 sheet: 0.55 (1.22), residues: 19 loop : 0.30 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.006 0.002 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 273) hydrogen bonds : angle 4.68052 ( 762) covalent geometry : bond 0.00448 ( 5193) covalent geometry : angle 0.63167 ( 7029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.613 Fit side-chains REVERT: H 249 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: I 242 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.4532 (mmt180) REVERT: I 260 LYS cc_start: 0.7102 (tttm) cc_final: 0.6894 (ttpp) REVERT: I 261 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7356 (ptmm) REVERT: J 14 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6752 (tttm) REVERT: J 99 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6594 (tt0) REVERT: J 293 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7808 (mptt) outliers start: 17 outliers final: 7 residues processed: 96 average time/residue: 1.3541 time to fit residues: 135.0327 Evaluate side-chains 96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.164180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145157 restraints weight = 4743.749| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.07 r_work: 0.3625 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.156 Angle : 0.595 8.705 7029 Z= 0.303 Chirality : 0.043 0.155 772 Planarity : 0.005 0.040 897 Dihedral : 7.087 77.802 703 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 2.73 % Allowed : 14.73 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.34), residues: 612 helix: 1.82 (0.28), residues: 341 sheet: 0.50 (1.21), residues: 19 loop : 0.34 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.007 0.001 HIS J 258 PHE 0.019 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 273) hydrogen bonds : angle 4.59744 ( 762) covalent geometry : bond 0.00356 ( 5193) covalent geometry : angle 0.59461 ( 7029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.623 Fit side-chains REVERT: H 249 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: I 260 LYS cc_start: 0.7124 (tttm) cc_final: 0.6922 (ttpp) REVERT: I 261 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (ptmm) REVERT: J 14 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6724 (tttm) REVERT: J 99 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: J 293 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7796 (mptt) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 1.4310 time to fit residues: 138.0304 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145088 restraints weight = 4747.097| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.06 r_work: 0.3625 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.155 Angle : 0.595 8.661 7029 Z= 0.302 Chirality : 0.043 0.155 772 Planarity : 0.005 0.040 897 Dihedral : 7.068 77.804 703 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.73 % Allowed : 14.91 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 612 helix: 1.84 (0.28), residues: 341 sheet: 0.54 (1.21), residues: 19 loop : 0.34 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 273) hydrogen bonds : angle 4.58831 ( 762) covalent geometry : bond 0.00353 ( 5193) covalent geometry : angle 0.59481 ( 7029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6330.46 seconds wall clock time: 116 minutes 43.52 seconds (7003.52 seconds total)