Starting phenix.real_space_refine on Thu Nov 14 09:18:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_17508.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_17508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_17508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_17508.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/11_2024/8p6v_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-5513/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: 4.05, per 1000 atoms: 0.77 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: 1.39 Conformation dependent library (CDL) restraints added in 604.0 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: 0.49 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: 1.35 Time building geometry restraints manager: 1.55 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.210 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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 : 0.574 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.4271 time to fit residues: 136.3226 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 : 0.613 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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: 0.6275 (tppt) cc_final: 0.5927 (tppt) REVERT: J 169 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5745 (m-80) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 1.4183 time to fit residues: 147.0615 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 : 0.616 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5229 Z= 0.219 Angle : 0.591 7.608 7077 Z= 0.305 Chirality : 0.043 0.139 777 Planarity : 0.005 0.032 903 Dihedral : 7.586 89.636 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.55 (0.34), residues: 618 helix: 1.83 (0.28), residues: 341 sheet: 0.21 (1.19), residues: 20 loop : 0.09 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.013 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.640 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 1.4675 time to fit residues: 146.1118 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5229 Z= 0.168 Angle : 0.550 7.438 7077 Z= 0.283 Chirality : 0.041 0.138 777 Planarity : 0.004 0.030 903 Dihedral : 7.463 88.660 708 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.07 % Allowed : 13.54 % 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: 1.78 (0.34), residues: 618 helix: 2.03 (0.28), residues: 341 sheet: 1.88 (1.54), residues: 15 loop : 0.04 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS H 259 PHE 0.013 0.001 PHE I 30 TYR 0.017 0.002 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.572 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 1.4169 time to fit residues: 147.2148 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5229 Z= 0.350 Angle : 0.710 9.327 7077 Z= 0.367 Chirality : 0.048 0.147 777 Planarity : 0.006 0.035 903 Dihedral : 7.740 89.996 708 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.61 % Allowed : 12.64 % 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: 1.06 (0.33), residues: 618 helix: 1.40 (0.27), residues: 341 sheet: -0.50 (1.07), residues: 20 loop : -0.03 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.015 0.003 PHE J 156 TYR 0.023 0.003 TYR I 2 ARG 0.005 0.001 ARG I 28 *********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.608 Fit side-chains REVERT: J 62 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6717 (tt0) outliers start: 20 outliers final: 9 residues processed: 104 average time/residue: 1.3883 time to fit residues: 149.8183 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS 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 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 227 GLU 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 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5229 Z= 0.203 Angle : 0.588 7.405 7077 Z= 0.304 Chirality : 0.042 0.143 777 Planarity : 0.005 0.033 903 Dihedral : 7.581 89.429 708 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.21 % 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: 1.39 (0.34), residues: 618 helix: 1.73 (0.28), residues: 340 sheet: 0.79 (1.18), residues: 15 loop : -0.07 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.002 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.605 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 95 average time/residue: 1.4888 time to fit residues: 146.6341 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 25 THR 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 43 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5229 Z= 0.350 Angle : 0.711 8.834 7077 Z= 0.368 Chirality : 0.048 0.149 777 Planarity : 0.006 0.035 903 Dihedral : 7.783 89.727 708 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 13.72 % 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: 0.88 (0.33), residues: 618 helix: 1.26 (0.27), residues: 341 sheet: -0.72 (1.05), residues: 20 loop : -0.12 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.015 0.003 PHE J 156 TYR 0.024 0.003 TYR I 2 ARG 0.004 0.001 ARG I 28 *********************** 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.629 Fit side-chains REVERT: I 141 GLU cc_start: 0.6989 (tp30) cc_final: 0.6564 (tp30) REVERT: J 62 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6717 (tt0) outliers start: 16 outliers final: 7 residues processed: 100 average time/residue: 1.5578 time to fit residues: 161.3928 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS 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 11 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1114 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= 0.219 Angle : 0.609 7.357 7077 Z= 0.315 Chirality : 0.043 0.144 777 Planarity : 0.005 0.034 903 Dihedral : 7.627 89.639 708 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 14.44 % Favored : 83.21 % 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: 1.24 (0.33), residues: 618 helix: 1.62 (0.27), residues: 341 sheet: 0.65 (1.20), residues: 15 loop : -0.18 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.007 0.002 HIS H 259 PHE 0.014 0.002 PHE I 110 TYR 0.017 0.002 TYR I 91 ARG 0.003 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.608 Fit side-chains REVERT: I 141 GLU cc_start: 0.7008 (tp30) cc_final: 0.6578 (tp30) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 1.5303 time to fit residues: 150.7587 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 : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR 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 24 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5229 Z= 0.204 Angle : 0.589 7.028 7077 Z= 0.302 Chirality : 0.042 0.141 777 Planarity : 0.004 0.034 903 Dihedral : 7.553 89.020 708 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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: 1.44 (0.34), residues: 618 helix: 1.80 (0.28), residues: 340 sheet: 0.86 (1.21), residues: 15 loop : -0.11 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 132 HIS 0.007 0.002 HIS H 259 PHE 0.014 0.002 PHE I 110 TYR 0.017 0.002 TYR I 91 ARG 0.004 0.000 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.643 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 1.4838 time to fit residues: 140.0368 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5229 Z= 0.229 Angle : 0.613 7.923 7077 Z= 0.317 Chirality : 0.043 0.142 777 Planarity : 0.005 0.034 903 Dihedral : 7.599 88.718 708 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 14.80 % Favored : 83.21 % 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: 1.28 (0.33), residues: 618 helix: 1.66 (0.28), residues: 340 sheet: 0.66 (1.18), residues: 15 loop : -0.15 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.008 0.002 HIS H 259 PHE 0.013 0.002 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.008 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.610 Fit side-chains REVERT: I 141 GLU cc_start: 0.6999 (tp30) cc_final: 0.6558 (tp30) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 1.4698 time to fit residues: 141.7304 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 I 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.174899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152330 restraints weight = 4764.190| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.97 r_work: 0.3743 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5229 Z= 0.295 Angle : 0.670 8.675 7077 Z= 0.346 Chirality : 0.045 0.146 777 Planarity : 0.005 0.034 903 Dihedral : 7.706 89.293 708 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 14.80 % 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: 1.01 (0.33), residues: 618 helix: 1.42 (0.27), residues: 341 sheet: 0.33 (1.16), residues: 15 loop : -0.24 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 132 HIS 0.008 0.002 HIS H 259 PHE 0.013 0.002 PHE I 110 TYR 0.021 0.002 TYR I 2 ARG 0.003 0.001 ARG I 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.65 seconds wall clock time: 53 minutes 41.38 seconds (3221.38 seconds total)