Starting phenix.real_space_refine on Tue Feb 11 10:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6y_17511/02_2025/8p6y_17511.cif" } resolution = 1.9 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3279 2.51 5 N 869 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5266 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 4.44, per 1000 atoms: 0.84 Number of scatterers: 5266 At special positions: 0 Unit cell: (84.7875, 94.7625, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1082 8.00 N 869 7.00 C 3279 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: 1.53 Conformation dependent library (CDL) restraints added in 638.7 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: 36 helices and 3 sheets defined 63.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.883A 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 removed outlier: 3.546A 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: 3.983A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.703A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.622A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.571A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.613A 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 200 Processing helix chain 'I' and resid 201 through 206 removed outlier: 4.519A pdb=" N TYR I 204 " --> pdb=" O THR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.743A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.539A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' Processing helix chain 'I' and resid 241 through 261 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: 4.435A 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: 3.886A 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: 3.824A 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 19 removed outlier: 7.149A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.974A 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 134 274 hydrogen bonds defined for protein. 759 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: 1.35 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1669 1.36 - 1.50: 1384 1.50 - 1.64: 2120 1.64 - 1.78: 7 1.78 - 1.91: 50 Bond restraints: 5230 Sorted by residual: bond pdb=" C6 AGS J 401 " pdb=" N6 AGS J 401 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C1' AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 1.459 1.319 0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" O3B AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sigma weight residual 1.559 1.656 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " ideal model delta sigma weight residual 1.386 1.338 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 5225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6949 1.77 - 3.53: 105 3.53 - 5.30: 22 5.30 - 7.06: 5 7.06 - 8.83: 4 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N1 AGS J 401 " pdb=" C2 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " ideal model delta sigma weight residual 103.67 107.94 -4.27 4.26e-01 5.51e+00 1.01e+02 angle pdb=" C5 AGS J 401 " pdb=" C4 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 126.80 119.81 6.99 7.41e-01 1.82e+00 8.90e+01 angle pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 114.03 108.21 5.82 6.99e-01 2.05e+00 6.93e+01 angle pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 110.73 108.03 2.70 4.52e-01 4.89e+00 3.57e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 2818 19.94 - 39.88: 257 39.88 - 59.81: 73 59.81 - 79.75: 11 79.75 - 99.69: 8 Dihedral angle restraints: 3167 sinusoidal: 1320 harmonic: 1847 Sorted by residual: dihedral pdb=" O1B AGS J 401 " pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sinusoidal sigma weight residual 68.91 168.60 -99.69 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 90.26 -90.26 1 3.00e+01 1.11e-03 1.07e+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 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 613 0.047 - 0.094: 131 0.094 - 0.142: 34 0.142 - 0.189: 1 0.189 - 0.236: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" C1' AGS J 401 " pdb=" C2' AGS J 401 " pdb=" N9 AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' AGS J 401 " pdb=" C1' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" O2' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.87 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C4' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" C5' AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.63 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 778 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 66 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" CD GLU I 66 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU I 66 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU I 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO I 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO J 140 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 186 2.70 - 3.25: 5265 3.25 - 3.80: 9244 3.80 - 4.35: 12178 4.35 - 4.90: 19355 Nonbonded interactions: 46228 Sorted by model distance: nonbonded pdb="MG MG J 402 " pdb=" O HOH J 551 " model vdw 2.148 2.170 nonbonded pdb=" O ARG I 242 " pdb=" NH1 ARG I 242 " model vdw 2.203 3.120 nonbonded pdb=" O HOH J 535 " pdb=" O HOH J 561 " model vdw 2.246 3.040 nonbonded pdb=" O HOH I 402 " pdb=" O HOH I 467 " model vdw 2.255 3.040 nonbonded pdb=" O HOH J 505 " pdb=" O HOH J 539 " model vdw 2.260 3.040 ... (remaining 46223 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: 3.610 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.820 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.005 0.140 5230 Z= 0.353 Angle : 0.600 8.826 7085 Z= 0.400 Chirality : 0.042 0.236 781 Planarity : 0.004 0.036 902 Dihedral : 17.032 99.688 1971 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 15.34 % Favored : 84.30 % 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: 1.99 (0.34), residues: 618 helix: 2.21 (0.29), residues: 331 sheet: -0.61 (1.27), residues: 19 loop : 0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 11 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.002 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.002 0.000 ARG I 188 *********************** 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 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.581 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 1.7506 time to fit residues: 162.6013 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133273 restraints weight = 4437.771| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 0.81 r_work: 0.3404 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5230 Z= 0.243 Angle : 0.639 8.309 7085 Z= 0.328 Chirality : 0.044 0.169 781 Planarity : 0.005 0.035 902 Dihedral : 8.191 90.930 712 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.84 % 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: 1.86 (0.34), residues: 618 helix: 2.13 (0.28), residues: 338 sheet: -0.46 (0.99), residues: 25 loop : 0.27 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.019 0.002 TYR I 2 ARG 0.004 0.001 ARG J 61 *********************** 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.577 Fit side-chains REVERT: I 234 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7082 (mp0) outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 1.7304 time to fit residues: 164.3776 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134443 restraints weight = 4464.190| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.82 r_work: 0.3419 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5230 Z= 0.173 Angle : 0.555 8.424 7085 Z= 0.285 Chirality : 0.041 0.137 781 Planarity : 0.004 0.034 902 Dihedral : 7.712 84.781 710 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % 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: 1.99 (0.34), residues: 618 helix: 2.30 (0.28), residues: 338 sheet: -0.34 (0.98), residues: 25 loop : 0.22 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.003 0.000 ARG J 61 *********************** 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.568 Fit side-chains REVERT: I 234 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7063 (mp0) REVERT: J 52 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6742 (mmtm) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 1.6709 time to fit residues: 167.3909 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134058 restraints weight = 4551.905| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 0.84 r_work: 0.3413 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5230 Z= 0.187 Angle : 0.577 8.473 7085 Z= 0.295 Chirality : 0.042 0.140 781 Planarity : 0.005 0.034 902 Dihedral : 7.547 80.829 709 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.44 % Allowed : 13.90 % Favored : 84.66 % 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: 618 helix: 2.27 (0.28), residues: 338 sheet: -0.33 (0.96), residues: 25 loop : 0.21 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.004 0.000 ARG J 188 *********************** 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.625 Fit side-chains REVERT: I 18 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: J 52 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6751 (mmtm) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 1.8062 time to fit residues: 173.1260 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.160148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136033 restraints weight = 4502.181| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.82 r_work: 0.3441 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5230 Z= 0.141 Angle : 0.527 9.043 7085 Z= 0.268 Chirality : 0.040 0.135 781 Planarity : 0.004 0.033 902 Dihedral : 7.350 79.185 709 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.44 % Allowed : 14.62 % Favored : 83.94 % 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: 2.14 (0.34), residues: 618 helix: 2.45 (0.28), residues: 338 sheet: -0.17 (0.96), residues: 25 loop : 0.24 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.001 PHE I 30 TYR 0.016 0.001 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.586 Fit side-chains REVERT: I 18 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: J 52 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6797 (mmtm) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 1.6667 time to fit residues: 168.5528 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133161 restraints weight = 4495.043| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.83 r_work: 0.3402 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5230 Z= 0.260 Angle : 0.650 8.721 7085 Z= 0.331 Chirality : 0.045 0.167 781 Planarity : 0.005 0.034 902 Dihedral : 7.549 78.251 709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 14.62 % Favored : 84.12 % 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: 2.13 (0.27), residues: 338 sheet: -0.46 (0.96), residues: 25 loop : 0.21 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.017 0.003 PHE I 71 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG J 188 *********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.570 Fit side-chains REVERT: I 18 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: J 52 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6791 (mmtm) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 1.8080 time to fit residues: 169.4589 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134085 restraints weight = 4477.263| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.83 r_work: 0.3415 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5230 Z= 0.205 Angle : 0.606 10.128 7085 Z= 0.308 Chirality : 0.043 0.151 781 Planarity : 0.005 0.034 902 Dihedral : 7.499 78.713 709 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 14.62 % Favored : 84.30 % 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: 1.89 (0.34), residues: 618 helix: 2.19 (0.28), residues: 338 sheet: -0.36 (0.96), residues: 25 loop : 0.21 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 *********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.967 Fit side-chains REVERT: I 18 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: J 52 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6764 (mmtm) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 1.7803 time to fit residues: 169.1977 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135952 restraints weight = 4505.278| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.82 r_work: 0.3440 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.002 0.031 5230 Z= 0.151 Angle : 0.550 10.836 7085 Z= 0.278 Chirality : 0.041 0.142 781 Planarity : 0.004 0.034 902 Dihedral : 7.324 77.804 709 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 0.90 % Allowed : 14.80 % Favored : 84.30 % 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: 2.11 (0.34), residues: 618 helix: 2.41 (0.28), residues: 338 sheet: -0.15 (0.96), residues: 25 loop : 0.24 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.002 PHE I 110 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.669 Fit side-chains REVERT: I 18 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (tt0) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 1.7975 time to fit residues: 168.6664 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.157043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132732 restraints weight = 4461.419| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.82 r_work: 0.3398 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.005 0.043 5230 Z= 0.319 Angle : 0.722 9.435 7085 Z= 0.369 Chirality : 0.047 0.175 781 Planarity : 0.005 0.036 902 Dihedral : 7.650 78.033 709 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 14.26 % Favored : 84.30 % 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: 1.49 (0.33), residues: 618 helix: 1.86 (0.27), residues: 344 sheet: -0.53 (0.95), residues: 25 loop : -0.01 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.011 0.002 HIS J 131 PHE 0.019 0.003 PHE I 13 TYR 0.022 0.003 TYR I 91 ARG 0.005 0.001 ARG J 188 *********************** 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 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.475 Fit side-chains REVERT: I 18 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7998 (tt0) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.7527 time to fit residues: 167.8750 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135941 restraints weight = 4526.300| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 0.83 r_work: 0.3442 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5230 Z= 0.155 Angle : 0.570 10.377 7085 Z= 0.290 Chirality : 0.042 0.149 781 Planarity : 0.004 0.033 902 Dihedral : 7.381 78.461 709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.72 % Allowed : 15.16 % Favored : 84.12 % 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: 2.01 (0.34), residues: 618 helix: 2.32 (0.28), residues: 338 sheet: -0.28 (0.94), residues: 25 loop : 0.22 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 11 HIS 0.010 0.001 HIS J 258 PHE 0.013 0.001 PHE I 110 TYR 0.014 0.001 TYR I 91 ARG 0.002 0.000 ARG I 188 ********************** 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 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.639 Fit side-chains REVERT: I 18 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7973 (tt0) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 1.8543 time to fit residues: 170.2083 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134883 restraints weight = 4535.324| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.83 r_work: 0.3428 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5230 Z= 0.184 Angle : 0.594 9.632 7085 Z= 0.302 Chirality : 0.042 0.143 781 Planarity : 0.004 0.034 902 Dihedral : 7.404 77.346 709 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 0.90 % Allowed : 14.98 % Favored : 84.12 % 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: 2.01 (0.34), residues: 618 helix: 2.30 (0.28), residues: 338 sheet: -0.35 (0.94), residues: 25 loop : 0.24 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6379.17 seconds wall clock time: 112 minutes 51.10 seconds (6771.10 seconds total)