Starting phenix.real_space_refine on Thu Mar 6 07:36:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6v_17508/03_2025/8p6v_17508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6v_17508/03_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_17508/03_2025/8p6v_17508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6v_17508/03_2025/8p6v_17508.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6v_17508/03_2025/8p6v_17508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6v_17508/03_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-5624/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: 4.68, 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: 1.31 Conformation dependent library (CDL) restraints added in 619.5 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: 0.50 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: 1.39 Time building geometry restraints manager: 1.53 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: 3.630 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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 : 0.602 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.3716 time to fit residues: 131.0402 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 : 0.630 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 0.9990 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: 0.7794 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.177410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154898 restraints weight = 4758.713| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 0.99 r_work: 0.3771 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0888 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= 0.171 Angle : 0.548 6.757 7077 Z= 0.284 Chirality : 0.041 0.131 777 Planarity : 0.004 0.030 903 Dihedral : 8.115 89.528 717 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % 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: 1.84 (0.35), residues: 618 helix: 2.06 (0.28), residues: 340 sheet: 0.81 (1.41), residues: 20 loop : 0.20 (0.40), residues: 258 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 0.013 0.001 PHE I 30 TYR 0.016 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 : 0.868 Fit side-chains REVERT: J 14 LYS cc_start: 0.6315 (tppt) cc_final: 0.5922 (tppt) REVERT: J 169 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5786 (m-80) outliers start: 18 outliers final: 6 residues processed: 99 average time/residue: 1.4781 time to fit residues: 151.6861 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 : 0.576 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152471 restraints weight = 4773.221| |-----------------------------------------------------------------------------| 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: 2.57 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1036 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= 0.270 Angle : 0.640 7.967 7077 Z= 0.331 Chirality : 0.044 0.142 777 Planarity : 0.005 0.033 903 Dihedral : 7.666 89.480 708 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 13.18 % 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: 1.39 (0.34), residues: 618 helix: 1.69 (0.28), residues: 341 sheet: -0.03 (1.13), residues: 20 loop : 0.04 (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 0.020 0.002 TYR I 2 ARG 0.005 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 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.548 Fit side-chains REVERT: I 141 GLU cc_start: 0.7081 (tp30) cc_final: 0.6660 (tp30) REVERT: J 27 TYR cc_start: 0.7457 (m-80) cc_final: 0.7114 (m-80) REVERT: J 62 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6727 (tt0) outliers start: 16 outliers final: 7 residues processed: 98 average time/residue: 1.4626 time to fit residues: 148.3370 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 : 0.548 ------------------------------------------------------------------------------- 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 I residue 261 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: 0.2980 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.177261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154522 restraints weight = 4889.519| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 0.99 r_work: 0.3767 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.029 5229 Z= 0.186 Angle : 0.566 6.665 7077 Z= 0.293 Chirality : 0.041 0.140 777 Planarity : 0.004 0.032 903 Dihedral : 7.526 89.247 708 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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: 1.63 (0.34), residues: 618 helix: 1.92 (0.28), residues: 341 sheet: 1.52 (1.34), residues: 15 loop : -0.01 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.013 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.003 0.000 ARG H 268 *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.558 Fit side-chains REVERT: I 75 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: I 242 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5768 (ptm-80) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 1.5202 time to fit residues: 154.4664 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 219 SER Chi-restraints excluded: chain I residue 242 ARG 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 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.177933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155456 restraints weight = 4825.513| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 0.98 r_work: 0.3779 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5229 Z= 0.167 Angle : 0.540 6.667 7077 Z= 0.278 Chirality : 0.041 0.137 777 Planarity : 0.004 0.031 903 Dihedral : 7.429 88.109 708 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 13.18 % 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: 2.12 (0.28), residues: 339 sheet: 1.81 (1.53), residues: 15 loop : -0.06 (0.38), residues: 264 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 0.016 0.002 TYR I 91 ARG 0.005 0.000 ARG I 279 *********************** 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.602 Fit side-chains REVERT: I 75 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7468 (ttm) outliers start: 19 outliers final: 8 residues processed: 104 average time/residue: 1.3927 time to fit residues: 150.3077 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET 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 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: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157108 restraints weight = 4840.882| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 0.99 r_work: 0.3798 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5229 Z= 0.145 Angle : 0.525 6.966 7077 Z= 0.270 Chirality : 0.040 0.135 777 Planarity : 0.004 0.030 903 Dihedral : 7.385 87.064 708 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.89 % Allowed : 14.08 % 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: 1.89 (0.34), residues: 618 helix: 2.20 (0.28), residues: 339 sheet: 1.88 (1.55), residues: 15 loop : -0.01 (0.38), residues: 264 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 0.015 0.002 TYR I 91 ARG 0.005 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.546 Fit side-chains REVERT: I 241 ASN cc_start: 0.4368 (OUTLIER) cc_final: 0.4163 (t0) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 1.4456 time to fit residues: 149.8837 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 253 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: 0.9980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.176429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153682 restraints weight = 4744.326| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 0.98 r_work: 0.3758 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5229 Z= 0.222 Angle : 0.597 8.484 7077 Z= 0.307 Chirality : 0.043 0.138 777 Planarity : 0.005 0.045 903 Dihedral : 7.313 87.934 707 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 14.44 % 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: 1.65 (0.34), residues: 618 helix: 1.86 (0.28), residues: 340 sheet: 0.26 (1.23), residues: 20 loop : 0.22 (0.40), residues: 258 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 0.012 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.616 Fit side-chains REVERT: I 141 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6761 (tp30) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 1.5223 time to fit residues: 151.7146 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 : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 236 LEU 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 52 LYS 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: 7.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.175203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152478 restraints weight = 4732.030| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.97 r_work: 0.3745 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5229 Z= 0.294 Angle : 0.671 9.519 7077 Z= 0.346 Chirality : 0.045 0.143 777 Planarity : 0.005 0.048 903 Dihedral : 7.489 89.071 707 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 13.36 % 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: 1.16 (0.33), residues: 618 helix: 1.48 (0.27), residues: 341 sheet: 0.82 (1.22), residues: 15 loop : -0.09 (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 J 131 PHE 0.013 0.002 PHE J 156 TYR 0.022 0.002 TYR I 91 ARG 0.006 0.001 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.567 Fit side-chains REVERT: I 141 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6697 (tp30) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 1.5124 time to fit residues: 147.0934 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 236 LEU 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 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: 4.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.175851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153158 restraints weight = 4779.537| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.97 r_work: 0.3751 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5229 Z= 0.250 Angle : 0.632 9.028 7077 Z= 0.325 Chirality : 0.044 0.143 777 Planarity : 0.005 0.041 903 Dihedral : 7.397 89.186 707 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.67 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: 1.21 (0.33), residues: 618 helix: 1.54 (0.27), residues: 341 sheet: 0.80 (1.23), residues: 15 loop : -0.09 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.013 0.002 PHE I 30 TYR 0.020 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.571 Fit side-chains REVERT: I 141 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: I 279 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6826 (mtm110) outliers start: 13 outliers final: 7 residues processed: 92 average time/residue: 1.6333 time to fit residues: 155.4983 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 236 LEU 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 17 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151760 restraints weight = 4759.694| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 0.97 r_work: 0.3737 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5229 Z= 0.331 Angle : 0.713 10.011 7077 Z= 0.369 Chirality : 0.047 0.146 777 Planarity : 0.006 0.039 903 Dihedral : 7.568 89.891 707 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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: 0.85 (0.33), residues: 618 helix: 1.24 (0.27), residues: 341 sheet: -0.56 (1.06), residues: 20 loop : -0.16 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.014 0.003 PHE J 156 TYR 0.023 0.003 TYR I 91 ARG 0.005 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.556 Fit side-chains REVERT: I 141 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6698 (tp30) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 1.4710 time to fit residues: 138.7669 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 236 LEU 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 37 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.177646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155029 restraints weight = 4804.458| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 0.97 r_work: 0.3774 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1226 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= 0.180 Angle : 0.582 7.752 7077 Z= 0.297 Chirality : 0.042 0.144 777 Planarity : 0.004 0.033 903 Dihedral : 7.300 89.031 707 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 15.88 % 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: 1.47 (0.34), residues: 618 helix: 1.84 (0.28), residues: 338 sheet: -0.06 (1.14), residues: 20 loop : -0.02 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.008 0.001 HIS H 259 PHE 0.014 0.001 PHE I 30 TYR 0.016 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: 6120.59 seconds wall clock time: 104 minutes 28.95 seconds (6268.95 seconds total)