Starting phenix.real_space_refine on Fri Dec 27 14:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.map" model { file = "/net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p70_17513/12_2024/8p70_17513.cif" } resolution = 2.0 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= 0.001 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 31 5.16 5 C 3309 2.51 5 N 876 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5282 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: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 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: 52 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AX4Q J 401 " occ=0.81 ... (50 atoms not shown) pdb=" N25BX4Q J 401 " occ=0.19 Time building chain proxies: 4.77, per 1000 atoms: 0.90 Number of scatterers: 5282 At special positions: 0 Unit cell: (84.7875, 93.3375, 66.975, 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 31 16.00 O 1066 8.00 N 876 7.00 C 3309 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: 1.34 Conformation dependent library (CDL) restraints added in 587.7 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 62.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 263 through 267 removed outlier: 3.514A pdb=" N LEU H 266 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 263 through 267' Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.537A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.834A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.621A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.543A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.982A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.794A 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: 4.622A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.465A 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: 3.649A 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 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.419A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 removed outlier: 3.869A pdb=" N ILE I 251 " --> pdb=" O GLN I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 284 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: 4.366A 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: 3.514A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 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: 3.707A 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 13 through 20 removed outlier: 6.552A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.864A 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 134 272 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: 1.40 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1644 1.34 - 1.46: 1122 1.46 - 1.58: 2438 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5255 Sorted by residual: bond pdb=" C15BX4Q J 401 " pdb=" N16BX4Q J 401 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C15AX4Q J 401 " pdb=" N16AX4Q J 401 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C02BX4Q J 401 " pdb=" C04BX4Q J 401 " ideal model delta sigma weight residual 1.496 1.598 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C02AX4Q J 401 " pdb=" C04AX4Q J 401 " ideal model delta sigma weight residual 1.496 1.598 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C07AX4Q J 401 " pdb=" N08AX4Q J 401 " ideal model delta sigma weight residual 1.367 1.453 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 5250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 6917 1.52 - 3.05: 141 3.05 - 4.57: 39 4.57 - 6.10: 10 6.10 - 7.62: 6 Bond angle restraints: 7113 Sorted by residual: angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N MET I 237 " pdb=" CA MET I 237 " pdb=" CB MET I 237 " ideal model delta sigma weight residual 113.65 109.48 4.17 1.47e+00 4.63e-01 8.06e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.27 4.63 1.80e+00 3.09e-01 6.63e+00 angle pdb=" CB MET I 75 " pdb=" CG MET I 75 " pdb=" SD MET I 75 " ideal model delta sigma weight residual 112.70 106.11 6.59 3.00e+00 1.11e-01 4.83e+00 angle pdb=" C PHE I 90 " pdb=" N TYR I 91 " pdb=" CA TYR I 91 " ideal model delta sigma weight residual 122.56 118.83 3.73 1.72e+00 3.38e-01 4.69e+00 ... (remaining 7108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 2879 22.38 - 44.77: 252 44.77 - 67.15: 35 67.15 - 89.53: 11 89.53 - 111.92: 2 Dihedral angle restraints: 3179 sinusoidal: 1332 harmonic: 1847 Sorted by residual: dihedral pdb=" C07BX4Q J 401 " pdb=" C09BX4Q J 401 " pdb=" N08BX4Q J 401 " pdb=" C10BX4Q J 401 " ideal model delta sinusoidal sigma weight residual 291.54 179.62 111.92 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C07BX4Q J 401 " pdb=" C09BX4Q J 401 " pdb=" N08BX4Q J 401 " pdb=" C13BX4Q J 401 " ideal model delta sinusoidal sigma weight residual 174.58 62.87 111.71 1 3.00e+01 1.11e-03 1.46e+01 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 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 472 0.029 - 0.058: 198 0.058 - 0.087: 59 0.087 - 0.116: 37 0.116 - 0.145: 11 Chirality restraints: 777 Sorted by residual: 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 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA PRO J 140 " pdb=" N PRO J 140 " pdb=" C PRO J 140 " pdb=" CB PRO J 140 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 774 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 237 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET I 237 " 0.030 2.00e-02 2.50e+03 pdb=" O MET I 237 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 238 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO I 50 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO J 140 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.021 5.00e-02 4.00e+02 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 529 2.74 - 3.28: 5489 3.28 - 3.82: 10018 3.82 - 4.36: 11931 4.36 - 4.90: 19411 Nonbonded interactions: 47378 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.202 3.040 nonbonded pdb=" O ARG I 9 " pdb=" O HOH I 401 " model vdw 2.208 3.040 nonbonded pdb=" O LEU I 144 " pdb=" O HOH I 402 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP J 104 " pdb=" OG SER J 106 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.235 3.040 ... (remaining 47373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.19 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: 2.770 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.050 Find NCS groups from input model: 0.070 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.006 0.134 5255 Z= 0.378 Angle : 0.617 7.621 7113 Z= 0.297 Chirality : 0.040 0.145 777 Planarity : 0.005 0.041 905 Dihedral : 16.718 111.917 1983 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % 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: 1.67 (0.34), residues: 618 helix: 1.97 (0.29), residues: 334 sheet: 0.84 (1.05), residues: 15 loop : 0.08 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 231 ARG 0.006 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.675 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 1.6305 time to fit residues: 160.7991 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5255 Z= 0.189 Angle : 0.534 6.407 7113 Z= 0.278 Chirality : 0.040 0.139 777 Planarity : 0.005 0.041 905 Dihedral : 7.326 92.203 725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 14.62 % Favored : 83.75 % 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: 1.83 (0.34), residues: 618 helix: 2.04 (0.29), residues: 345 sheet: 0.72 (1.08), residues: 15 loop : 0.18 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.642 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 102 average time/residue: 1.8082 time to fit residues: 190.9291 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5255 Z= 0.200 Angle : 0.557 8.542 7113 Z= 0.283 Chirality : 0.040 0.142 777 Planarity : 0.005 0.041 905 Dihedral : 6.466 64.512 722 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % Favored : 82.49 % 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: 1.77 (0.34), residues: 618 helix: 2.00 (0.28), residues: 345 sheet: 0.52 (1.09), residues: 15 loop : 0.15 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.686 Fit side-chains REVERT: I 260 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6758 (ttmt) outliers start: 11 outliers final: 5 residues processed: 108 average time/residue: 1.6636 time to fit residues: 185.6977 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 266 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.0000 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5255 Z= 0.208 Angle : 0.554 7.231 7113 Z= 0.284 Chirality : 0.040 0.143 777 Planarity : 0.005 0.042 905 Dihedral : 6.196 58.840 722 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 15.70 % Favored : 82.49 % 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: 1.76 (0.34), residues: 618 helix: 2.00 (0.28), residues: 345 sheet: 0.46 (1.13), residues: 15 loop : 0.14 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.682 Fit side-chains REVERT: I 260 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6727 (ttmt) outliers start: 10 outliers final: 4 residues processed: 104 average time/residue: 1.5734 time to fit residues: 169.4299 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5255 Z= 0.282 Angle : 0.618 6.622 7113 Z= 0.316 Chirality : 0.043 0.149 777 Planarity : 0.005 0.044 905 Dihedral : 6.531 58.098 722 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 15.52 % Favored : 81.95 % 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: 1.52 (0.34), residues: 618 helix: 1.78 (0.28), residues: 343 sheet: 0.44 (1.18), residues: 15 loop : 0.08 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.005 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.672 Fit side-chains REVERT: H 249 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.7004 (mm-40) REVERT: H 251 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5095 (mp) REVERT: I 77 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6110 (ptp-170) REVERT: I 250 ASP cc_start: 0.7195 (p0) cc_final: 0.6910 (m-30) REVERT: I 260 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6721 (ttmt) outliers start: 14 outliers final: 4 residues processed: 103 average time/residue: 1.5354 time to fit residues: 163.8678 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN J 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5255 Z= 0.168 Angle : 0.525 6.293 7113 Z= 0.271 Chirality : 0.040 0.141 777 Planarity : 0.005 0.042 905 Dihedral : 5.752 57.728 722 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 15.70 % Favored : 82.31 % 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: 1.87 (0.34), residues: 618 helix: 2.14 (0.28), residues: 344 sheet: 0.40 (1.16), residues: 15 loop : 0.14 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.590 Fit side-chains REVERT: I 77 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6060 (ptp-170) REVERT: I 260 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6785 (ttmt) outliers start: 11 outliers final: 4 residues processed: 104 average time/residue: 1.5263 time to fit residues: 164.6323 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5255 Z= 0.265 Angle : 0.614 10.333 7113 Z= 0.312 Chirality : 0.042 0.147 777 Planarity : 0.005 0.044 905 Dihedral : 6.199 56.487 722 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 15.70 % Favored : 81.95 % 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: 1.61 (0.34), residues: 618 helix: 1.86 (0.28), residues: 343 sheet: 0.42 (1.21), residues: 15 loop : 0.11 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.020 0.002 TYR I 231 ARG 0.006 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.627 Fit side-chains REVERT: H 249 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6980 (mm-40) REVERT: I 77 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6101 (ptp-170) REVERT: I 250 ASP cc_start: 0.7196 (p0) cc_final: 0.6923 (m-30) REVERT: I 260 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6778 (ttmt) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 1.6969 time to fit residues: 174.2654 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5255 Z= 0.206 Angle : 0.572 9.523 7113 Z= 0.291 Chirality : 0.041 0.146 777 Planarity : 0.005 0.043 905 Dihedral : 5.902 55.157 722 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.59 % 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: 618 helix: 1.96 (0.28), residues: 345 sheet: 0.35 (1.18), residues: 15 loop : 0.16 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.588 Fit side-chains REVERT: H 249 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6968 (mm-40) REVERT: I 77 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6078 (ptp-170) REVERT: I 250 ASP cc_start: 0.7175 (p0) cc_final: 0.6903 (m-30) REVERT: I 260 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6718 (ttmt) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 1.5330 time to fit residues: 160.3306 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5255 Z= 0.240 Angle : 0.597 9.135 7113 Z= 0.305 Chirality : 0.042 0.146 777 Planarity : 0.005 0.043 905 Dihedral : 6.069 55.876 722 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.17 % Allowed : 16.43 % Favored : 81.41 % 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: 1.63 (0.34), residues: 618 helix: 1.88 (0.28), residues: 343 sheet: 0.42 (1.21), residues: 15 loop : 0.11 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.021 0.002 TYR I 231 ARG 0.007 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.664 Fit side-chains REVERT: H 249 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6961 (mm-40) REVERT: I 77 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6085 (ptp-170) REVERT: I 250 ASP cc_start: 0.7175 (p0) cc_final: 0.6905 (m-30) REVERT: I 260 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6734 (ttmt) REVERT: J 293 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8020 (mtmt) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 1.5480 time to fit residues: 154.0865 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5255 Z= 0.162 Angle : 0.538 9.331 7113 Z= 0.275 Chirality : 0.040 0.144 777 Planarity : 0.005 0.043 905 Dihedral : 5.494 53.081 722 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 17.87 % Favored : 81.23 % 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 (0.35), residues: 618 helix: 2.18 (0.29), residues: 344 sheet: 0.38 (1.15), residues: 15 loop : 0.15 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.617 Fit side-chains REVERT: I 77 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6048 (ptp-170) REVERT: I 228 MET cc_start: 0.8044 (ptm) cc_final: 0.7763 (ptm) REVERT: I 260 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6768 (ttmt) outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 1.5299 time to fit residues: 153.7614 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141484 restraints weight = 23032.325| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.70 r_work: 0.3601 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5255 Z= 0.211 Angle : 0.579 6.774 7113 Z= 0.297 Chirality : 0.041 0.146 777 Planarity : 0.005 0.043 905 Dihedral : 5.726 54.856 722 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 17.51 % Favored : 81.41 % 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: 618 helix: 2.01 (0.29), residues: 345 sheet: 0.34 (1.15), residues: 15 loop : 0.19 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3088.65 seconds wall clock time: 56 minutes 33.73 seconds (3393.73 seconds total)