Starting phenix.real_space_refine on Tue Feb 11 11:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6v_17508/02_2025/8p6v_17508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6v_17508/02_2025/8p6v_17508.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/8p6v_17508/02_2025/8p6v_17508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6v_17508/02_2025/8p6v_17508.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6v_17508/02_2025/8p6v_17508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6v_17508/02_2025/8p6v_17508.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= 0.001 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 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5243 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'I74': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 4.69, per 1000 atoms: 0.89 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 94.05, 69.1125, 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 1051 8.00 N 870 7.00 C 3291 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 581.1 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 63.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.520A 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: 3.860A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.008A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.827A 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: 4.570A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.402A 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: 3.516A 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 235 removed outlier: 3.913A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 69 removed outlier: 4.136A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) 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 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.573A 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 removed outlier: 3.556A pdb=" N LEU J 243 " --> pdb=" O MET J 240 " (cutoff:3.500A) 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 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.655A 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 17 through 21 removed outlier: 5.582A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 25 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.866A 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 134 279 hydrogen bonds defined for protein. 780 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: 1.43 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1637 1.34 - 1.46: 969 1.46 - 1.58: 2572 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5229 Sorted by residual: bond pdb=" C3 I74 J 401 " pdb=" N10 I74 J 401 " ideal model delta sigma weight residual 1.335 1.489 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C26 I74 J 401 " pdb=" C8 I74 J 401 " ideal model delta sigma weight residual 1.497 1.602 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 I74 J 401 " pdb=" N18 I74 J 401 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C41 I74 J 401 " pdb=" C46 I74 J 401 " ideal model delta sigma weight residual 1.532 1.456 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C40 I74 J 401 " pdb=" C41 I74 J 401 " ideal model delta sigma weight residual 1.524 1.592 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 5224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6921 1.72 - 3.43: 124 3.43 - 5.15: 23 5.15 - 6.87: 8 6.87 - 8.59: 1 Bond angle restraints: 7077 Sorted by residual: angle pdb=" CA LYS I 260 " pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.68e+00 angle pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " pdb=" CD LYS J 293 " ideal model delta sigma weight residual 111.30 118.04 -6.74 2.30e+00 1.89e-01 8.59e+00 angle pdb=" CA GLU I 268 " pdb=" CB GLU I 268 " pdb=" CG GLU I 268 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " pdb=" CD LYS I 260 " ideal model delta sigma weight residual 111.30 116.85 -5.55 2.30e+00 1.89e-01 5.82e+00 ... (remaining 7072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2791 17.41 - 34.83: 270 34.83 - 52.24: 73 52.24 - 69.65: 17 69.65 - 87.06: 13 Dihedral angle restraints: 3164 sinusoidal: 1317 harmonic: 1847 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG J 176 " pdb=" CD ARG J 176 " pdb=" NE ARG J 176 " pdb=" CZ ARG J 176 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+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 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 445 0.028 - 0.057: 210 0.057 - 0.085: 75 0.085 - 0.114: 39 0.114 - 0.142: 8 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 5.05e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL H 260 " pdb=" N VAL H 260 " pdb=" C VAL H 260 " pdb=" CB VAL H 260 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 14 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LYS J 14 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS J 14 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU J 15 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 163 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C CYS J 201 " -0.021 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 836 2.76 - 3.29: 5304 3.29 - 3.83: 9756 3.83 - 4.36: 11745 4.36 - 4.90: 18996 Nonbonded interactions: 46637 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.221 3.040 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.225 3.040 nonbonded pdb=" O MET J 189 " pdb=" O HOH J 501 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR I 178 " pdb=" OG SER I 230 " model vdw 2.238 3.040 nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 571 " model vdw 2.243 3.040 ... (remaining 46632 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.050 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 0.154 5229 Z= 0.336 Angle : 0.616 8.587 7077 Z= 0.309 Chirality : 0.041 0.142 777 Planarity : 0.004 0.031 903 Dihedral : 16.303 87.063 1968 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 13.90 % 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: 1.53 (0.34), residues: 618 helix: 1.80 (0.28), residues: 337 sheet: 0.43 (1.28), residues: 20 loop : 0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.007 0.000 ARG H 268 *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.633 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.4533 time to fit residues: 138.7385 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.0030 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154145 restraints weight = 4749.550| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 0.98 r_work: 0.3761 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5229 Z= 0.188 Angle : 0.563 6.902 7077 Z= 0.292 Chirality : 0.042 0.135 777 Planarity : 0.004 0.031 903 Dihedral : 8.160 88.785 717 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.25 % Allowed : 12.82 % 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: 1.77 (0.34), residues: 618 helix: 1.99 (0.28), residues: 340 sheet: 0.64 (1.32), residues: 20 loop : 0.19 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.569 Fit side-chains REVERT: J 14 LYS cc_start: 0.6358 (tppt) cc_final: 0.5948 (tppt) REVERT: J 169 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5775 (m-80) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 1.4595 time to fit residues: 151.3007 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 : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.174926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152254 restraints weight = 4775.762| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.97 r_work: 0.3742 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5229 Z= 0.280 Angle : 0.649 8.217 7077 Z= 0.336 Chirality : 0.045 0.142 777 Planarity : 0.005 0.033 903 Dihedral : 7.679 89.372 708 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.07 % Allowed : 13.00 % 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: 1.32 (0.33), residues: 618 helix: 1.63 (0.27), residues: 341 sheet: -0.12 (1.11), residues: 20 loop : 0.02 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.021 0.002 TYR I 2 ARG 0.006 0.001 ARG H 268 *********************** 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.558 Fit side-chains REVERT: I 141 GLU cc_start: 0.7079 (tp30) cc_final: 0.6672 (tp30) REVERT: J 27 TYR cc_start: 0.7465 (m-80) cc_final: 0.7112 (m-80) REVERT: J 62 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6738 (tt0) outliers start: 17 outliers final: 6 residues processed: 99 average time/residue: 1.4802 time to fit residues: 151.7147 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156677 restraints weight = 4905.704| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 0.99 r_work: 0.3795 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5229 Z= 0.150 Angle : 0.531 6.274 7077 Z= 0.274 Chirality : 0.040 0.137 777 Planarity : 0.004 0.031 903 Dihedral : 7.409 88.042 708 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 13.90 % Favored : 83.39 % 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: 2.16 (0.28), residues: 339 sheet: 0.61 (1.38), residues: 20 loop : -0.00 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS H 259 PHE 0.013 0.001 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG I 279 *********************** 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: 15 poor density : 92 time to evaluate : 0.592 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 1.4552 time to fit residues: 152.4061 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156256 restraints weight = 4814.786| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.98 r_work: 0.3786 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5229 Z= 0.155 Angle : 0.528 6.755 7077 Z= 0.271 Chirality : 0.040 0.135 777 Planarity : 0.004 0.031 903 Dihedral : 7.107 88.418 707 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 13.72 % 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: 1.90 (0.34), residues: 618 helix: 2.22 (0.28), residues: 339 sheet: 0.58 (1.38), residues: 20 loop : 0.07 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.012 0.001 PHE I 30 TYR 0.016 0.001 TYR I 91 ARG 0.003 0.000 ARG I 242 *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.630 Fit side-chains REVERT: I 241 ASN cc_start: 0.4486 (OUTLIER) cc_final: 0.4271 (t0) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 1.4529 time to fit residues: 152.1363 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156145 restraints weight = 4835.385| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 0.99 r_work: 0.3786 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5229 Z= 0.165 Angle : 0.544 8.127 7077 Z= 0.279 Chirality : 0.041 0.136 777 Planarity : 0.004 0.032 903 Dihedral : 7.130 87.387 707 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.17 % Allowed : 14.26 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.34), residues: 618 helix: 2.12 (0.28), residues: 340 sheet: 1.96 (1.60), residues: 15 loop : 0.18 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.012 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.571 Fit side-chains REVERT: I 241 ASN cc_start: 0.4314 (OUTLIER) cc_final: 0.4085 (t0) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 1.5040 time to fit residues: 144.9742 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155233 restraints weight = 4743.652| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 0.98 r_work: 0.3776 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5229 Z= 0.182 Angle : 0.562 7.809 7077 Z= 0.287 Chirality : 0.041 0.138 777 Planarity : 0.004 0.036 903 Dihedral : 7.173 86.989 707 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 13.72 % Favored : 83.57 % 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: 2.05 (0.28), residues: 340 sheet: 0.65 (1.41), residues: 20 loop : 0.28 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.012 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.006 0.000 ARG I 279 *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.633 Fit side-chains REVERT: I 241 ASN cc_start: 0.4413 (OUTLIER) cc_final: 0.4176 (t0) REVERT: J 62 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6867 (tt0) outliers start: 15 outliers final: 7 residues processed: 99 average time/residue: 1.5235 time to fit residues: 156.4102 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156530 restraints weight = 4755.175| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 0.98 r_work: 0.3789 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5229 Z= 0.163 Angle : 0.550 7.889 7077 Z= 0.281 Chirality : 0.041 0.136 777 Planarity : 0.004 0.031 903 Dihedral : 7.099 86.458 707 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 15.16 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.34), residues: 618 helix: 2.18 (0.28), residues: 338 sheet: 1.98 (1.50), residues: 15 loop : 0.08 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.012 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.000 ARG I 279 *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.675 Fit side-chains REVERT: I 241 ASN cc_start: 0.4345 (OUTLIER) cc_final: 0.4101 (t0) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 1.5265 time to fit residues: 153.4382 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153503 restraints weight = 4797.943| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 0.98 r_work: 0.3756 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5229 Z= 0.242 Angle : 0.635 9.427 7077 Z= 0.325 Chirality : 0.043 0.138 777 Planarity : 0.005 0.057 903 Dihedral : 7.305 88.026 707 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.07 % Allowed : 14.08 % Favored : 82.85 % 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: 1.56 (0.34), residues: 618 helix: 1.79 (0.28), residues: 340 sheet: 0.15 (1.19), residues: 20 loop : 0.19 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.012 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.006 0.001 ARG I 279 *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.582 Fit side-chains REVERT: I 141 GLU cc_start: 0.7195 (tp30) cc_final: 0.6773 (tp30) REVERT: I 279 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6813 (mtm110) REVERT: J 62 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6880 (tt0) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 1.6075 time to fit residues: 161.3128 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 : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.177933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155259 restraints weight = 4795.600| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 0.98 r_work: 0.3776 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5229 Z= 0.182 Angle : 0.580 9.188 7077 Z= 0.298 Chirality : 0.042 0.139 777 Planarity : 0.004 0.039 903 Dihedral : 7.217 87.238 707 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 14.44 % Favored : 83.57 % 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: 1.68 (0.34), residues: 618 helix: 1.96 (0.28), residues: 338 sheet: 1.65 (1.46), residues: 15 loop : 0.04 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.012 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.001 ARG I 279 ********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.566 Fit side-chains REVERT: I 141 GLU cc_start: 0.7229 (tp30) cc_final: 0.6827 (tp30) REVERT: I 279 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6796 (mtm110) REVERT: J 62 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6862 (tt0) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 1.5617 time to fit residues: 153.5301 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155811 restraints weight = 4776.106| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 0.98 r_work: 0.3781 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5229 Z= 0.176 Angle : 0.562 7.397 7077 Z= 0.288 Chirality : 0.041 0.138 777 Planarity : 0.004 0.037 903 Dihedral : 7.147 86.985 707 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 14.80 % Favored : 83.39 % 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: 2.04 (0.28), residues: 338 sheet: 1.84 (1.53), residues: 15 loop : 0.03 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.008 0.001 HIS H 259 PHE 0.012 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.006 0.000 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5849.50 seconds wall clock time: 103 minutes 35.27 seconds (6215.27 seconds total)