Starting phenix.real_space_refine on Wed Mar 5 19:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.map" model { file = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m7d_30129/03_2025/6m7d_30129.cif" } resolution = 2.9 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= 0.006 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 14 5.16 5 C 2054 2.51 5 N 552 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 6.11, per 1000 atoms: 1.86 Number of scatterers: 3280 At special positions: 0 Unit cell: (78.52, 81.64, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 6 15.00 O 654 8.00 N 552 7.00 C 2054 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: 0.84 Conformation dependent library (CDL) restraints added in 338.6 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.5% alpha, 5.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.144A pdb=" N LYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.224A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.763A pdb=" N VAL A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 307 through 313 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 387 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.533A pdb=" N SER A 33 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 102 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 35 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 37 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 106 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LYS A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 105 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O TYR A 127 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 683 1.33 - 1.45: 765 1.45 - 1.57: 1863 1.57 - 1.69: 11 1.69 - 1.81: 26 Bond restraints: 3348 Sorted by residual: bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.85e+00 bond pdb=" N MET A 125 " pdb=" CA MET A 125 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.22e-02 6.72e+03 8.47e+00 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 3587 1.07 - 2.14: 622 2.14 - 3.22: 299 3.22 - 4.29: 40 4.29 - 5.36: 8 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CA ASP A 405 " pdb=" C ASP A 405 " pdb=" O ASP A 405 " ideal model delta sigma weight residual 122.63 118.22 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" N THR A 272 " pdb=" CA THR A 272 " pdb=" C THR A 272 " ideal model delta sigma weight residual 111.28 107.63 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C ASN A 241 " pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 120.28 124.74 -4.46 1.34e+00 5.57e-01 1.11e+01 angle pdb=" C SER A 402 " pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 120.00 123.63 -3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" O ARG A 149 " ideal model delta sigma weight residual 121.56 118.10 3.46 1.09e+00 8.42e-01 1.01e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1813 17.82 - 35.64: 159 35.64 - 53.46: 35 53.46 - 71.28: 15 71.28 - 89.10: 3 Dihedral angle restraints: 2025 sinusoidal: 847 harmonic: 1178 Sorted by residual: dihedral pdb=" C GLU A 278 " pdb=" N GLU A 278 " pdb=" CA GLU A 278 " pdb=" CB GLU A 278 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual -90.00 -159.31 69.31 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " pdb=" CD GLU A 214 " pdb=" OE1 GLU A 214 " ideal model delta sinusoidal sigma weight residual 0.00 89.10 -89.10 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 286 0.046 - 0.092: 152 0.092 - 0.139: 69 0.139 - 0.185: 17 0.185 - 0.231: 9 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 530 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.031 2.00e-02 2.50e+03 1.53e-02 5.25e+00 pdb=" N1 U B 2 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 240 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C MET A 240 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 241 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 44 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C VAL A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 115 2.71 - 3.25: 3405 3.25 - 3.80: 5504 3.80 - 4.35: 7360 4.35 - 4.90: 11397 Nonbonded interactions: 27781 Sorted by model distance: nonbonded pdb=" O ALA A 346 " pdb=" O2' U B 4 " model vdw 2.157 3.040 nonbonded pdb=" O THR A 183 " pdb=" O2' U B 2 " model vdw 2.198 3.040 nonbonded pdb=" O ALA A 325 " pdb=" ND2 ASN A 328 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN A 173 " pdb=" O LEU A 209 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP A 202 " pdb=" OG1 THR A 204 " model vdw 2.262 3.040 ... (remaining 27776 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: 15.360 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:18.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.056 3348 Z= 0.657 Angle : 1.033 5.361 4556 Z= 0.761 Chirality : 0.069 0.231 533 Planarity : 0.005 0.041 564 Dihedral : 14.955 89.104 1273 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.58 % Allowed : 13.12 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.38), residues: 410 helix: -0.14 (0.32), residues: 244 sheet: -0.49 (1.15), residues: 23 loop : -0.28 (0.41), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.004 0.001 HIS A 397 PHE 0.016 0.002 PHE A 193 TYR 0.011 0.002 TYR A 275 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.356 Fit side-chains REVERT: A 290 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7519 (ttp-110) REVERT: A 400 ASN cc_start: 0.8217 (m-40) cc_final: 0.7949 (m-40) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 1.3401 time to fit residues: 93.4682 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 93 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN A 227 GLN A 241 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 288 ASN A 366 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.147794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.123921 restraints weight = 3449.532| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.02 r_work: 0.2934 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.165 Angle : 0.481 4.806 4556 Z= 0.260 Chirality : 0.040 0.146 533 Planarity : 0.004 0.032 564 Dihedral : 9.680 60.088 541 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.33 % Allowed : 14.29 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.39), residues: 410 helix: 0.77 (0.33), residues: 247 sheet: -0.17 (1.02), residues: 23 loop : 0.36 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 333 HIS 0.004 0.001 HIS A 397 PHE 0.013 0.001 PHE A 269 TYR 0.008 0.001 TYR A 275 ARG 0.005 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.565 Fit side-chains REVERT: A 56 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8458 (p) REVERT: A 62 LEU cc_start: 0.9075 (mt) cc_final: 0.8827 (mm) REVERT: A 290 ARG cc_start: 0.8722 (ttt180) cc_final: 0.7613 (ttp-110) REVERT: A 345 LYS cc_start: 0.8300 (tppt) cc_final: 0.8033 (mmpt) REVERT: A 377 SER cc_start: 0.8858 (p) cc_final: 0.8600 (p) REVERT: A 400 ASN cc_start: 0.8234 (m-40) cc_final: 0.8010 (m-40) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 1.2548 time to fit residues: 74.8500 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.123086 restraints weight = 3333.309| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.12 r_work: 0.2857 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3348 Z= 0.161 Angle : 0.451 4.924 4556 Z= 0.241 Chirality : 0.039 0.117 533 Planarity : 0.003 0.031 564 Dihedral : 9.625 59.773 541 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.33 % Allowed : 15.16 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.40), residues: 410 helix: 1.17 (0.34), residues: 248 sheet: -0.35 (0.93), residues: 25 loop : 0.77 (0.47), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 PHE 0.012 0.001 PHE A 269 TYR 0.006 0.001 TYR A 275 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.360 Fit side-chains REVERT: A 56 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 290 ARG cc_start: 0.8662 (ttt180) cc_final: 0.7607 (ttp-110) REVERT: A 377 SER cc_start: 0.8812 (p) cc_final: 0.8543 (p) REVERT: A 400 ASN cc_start: 0.8160 (m-40) cc_final: 0.7924 (m-40) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 1.2133 time to fit residues: 68.7881 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.123308 restraints weight = 3429.218| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.96 r_work: 0.2883 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.172 Angle : 0.450 5.345 4556 Z= 0.239 Chirality : 0.039 0.117 533 Planarity : 0.003 0.030 564 Dihedral : 9.581 59.776 541 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.79 % Allowed : 13.99 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.41), residues: 410 helix: 1.42 (0.34), residues: 242 sheet: -0.41 (0.87), residues: 25 loop : 1.22 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 PHE 0.011 0.001 PHE A 269 TYR 0.006 0.001 TYR A 275 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.358 Fit side-chains REVERT: A 56 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 201 GLN cc_start: 0.6444 (OUTLIER) cc_final: 0.5826 (tt0) REVERT: A 290 ARG cc_start: 0.8612 (ttt180) cc_final: 0.7592 (ttp-110) REVERT: A 377 SER cc_start: 0.8795 (p) cc_final: 0.8536 (p) REVERT: A 400 ASN cc_start: 0.8146 (m-40) cc_final: 0.7882 (m-40) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 1.2668 time to fit residues: 72.0468 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.151587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.128415 restraints weight = 3458.282| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.94 r_work: 0.2968 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3348 Z= 0.123 Angle : 0.426 5.838 4556 Z= 0.226 Chirality : 0.038 0.121 533 Planarity : 0.003 0.030 564 Dihedral : 9.524 59.666 541 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.33 % Allowed : 15.16 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.41), residues: 410 helix: 1.69 (0.34), residues: 243 sheet: -0.33 (0.87), residues: 25 loop : 1.24 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.013 0.001 PHE A 269 TYR 0.007 0.001 TYR A 275 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.335 Fit side-chains REVERT: A 201 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5757 (tt0) REVERT: A 290 ARG cc_start: 0.8538 (ttt180) cc_final: 0.7562 (ttp-110) REVERT: A 377 SER cc_start: 0.8757 (p) cc_final: 0.8526 (p) REVERT: A 400 ASN cc_start: 0.8068 (m-40) cc_final: 0.7839 (m-40) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 1.1678 time to fit residues: 66.4323 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.150903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.127241 restraints weight = 3491.041| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.98 r_work: 0.2940 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3348 Z= 0.133 Angle : 0.449 8.074 4556 Z= 0.230 Chirality : 0.039 0.141 533 Planarity : 0.003 0.029 564 Dihedral : 9.480 59.557 541 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.62 % Allowed : 16.03 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.41), residues: 410 helix: 1.74 (0.34), residues: 243 sheet: -0.25 (0.87), residues: 25 loop : 1.28 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.012 0.001 PHE A 269 TYR 0.006 0.001 TYR A 275 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.327 Fit side-chains REVERT: A 201 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5790 (tt0) REVERT: A 290 ARG cc_start: 0.8568 (ttt180) cc_final: 0.7586 (ttp-110) REVERT: A 377 SER cc_start: 0.8769 (p) cc_final: 0.8529 (p) REVERT: A 400 ASN cc_start: 0.8136 (m-40) cc_final: 0.7885 (m-40) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 1.2142 time to fit residues: 65.2323 Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.144044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.120213 restraints weight = 3394.885| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.05 r_work: 0.2809 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3348 Z= 0.277 Angle : 0.524 6.952 4556 Z= 0.270 Chirality : 0.043 0.143 533 Planarity : 0.003 0.029 564 Dihedral : 9.624 59.950 541 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.62 % Allowed : 16.03 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.41), residues: 410 helix: 1.41 (0.34), residues: 240 sheet: 0.02 (0.90), residues: 25 loop : 1.42 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 PHE 0.010 0.002 PHE A 312 TYR 0.009 0.002 TYR A 260 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.337 Fit side-chains REVERT: A 290 ARG cc_start: 0.8669 (ttt180) cc_final: 0.7649 (ttp-110) REVERT: A 400 ASN cc_start: 0.8236 (m-40) cc_final: 0.7922 (m-40) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 1.2167 time to fit residues: 60.2501 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.124536 restraints weight = 3420.457| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.02 r_work: 0.2965 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.157 Angle : 0.468 7.289 4556 Z= 0.240 Chirality : 0.039 0.129 533 Planarity : 0.003 0.030 564 Dihedral : 9.513 59.738 541 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.33 % Allowed : 16.03 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 410 helix: 1.56 (0.34), residues: 242 sheet: 0.19 (0.90), residues: 25 loop : 1.46 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.011 0.001 PHE A 269 TYR 0.011 0.001 TYR A 127 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.333 Fit side-chains REVERT: A 290 ARG cc_start: 0.8751 (ttt180) cc_final: 0.7624 (ttp-110) REVERT: A 400 ASN cc_start: 0.8220 (m-40) cc_final: 0.7950 (m-40) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.1282 time to fit residues: 57.0883 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.147230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.122770 restraints weight = 3417.677| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.99 r_work: 0.2954 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3348 Z= 0.177 Angle : 0.479 7.489 4556 Z= 0.246 Chirality : 0.040 0.125 533 Planarity : 0.003 0.029 564 Dihedral : 9.506 59.781 541 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.46 % Allowed : 16.91 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 410 helix: 1.54 (0.34), residues: 242 sheet: 0.30 (0.89), residues: 25 loop : 1.47 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.010 0.001 PHE A 269 TYR 0.006 0.001 TYR A 303 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.376 Fit side-chains REVERT: A 290 ARG cc_start: 0.8690 (ttt180) cc_final: 0.7619 (ttp-110) REVERT: A 400 ASN cc_start: 0.8236 (m-40) cc_final: 0.7967 (m-40) outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 1.1500 time to fit residues: 53.4984 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.147441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.123197 restraints weight = 3371.492| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.97 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3348 Z= 0.172 Angle : 0.479 7.771 4556 Z= 0.245 Chirality : 0.040 0.125 533 Planarity : 0.003 0.029 564 Dihedral : 9.488 59.778 541 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.75 % Allowed : 16.62 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.41), residues: 410 helix: 1.55 (0.34), residues: 242 sheet: 0.39 (0.92), residues: 25 loop : 1.46 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.011 0.001 PHE A 269 TYR 0.011 0.001 TYR A 127 ARG 0.005 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.361 Fit side-chains REVERT: A 290 ARG cc_start: 0.8590 (ttt180) cc_final: 0.7622 (ttp-110) REVERT: A 400 ASN cc_start: 0.8161 (m-40) cc_final: 0.7908 (m-40) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 1.2144 time to fit residues: 57.6615 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.148154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.123857 restraints weight = 3402.106| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.96 r_work: 0.2907 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3348 Z= 0.161 Angle : 0.473 7.725 4556 Z= 0.242 Chirality : 0.039 0.122 533 Planarity : 0.003 0.029 564 Dihedral : 9.458 59.759 541 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.46 % Allowed : 16.91 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 410 helix: 1.58 (0.34), residues: 242 sheet: 0.48 (0.95), residues: 25 loop : 1.43 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 PHE 0.011 0.001 PHE A 269 TYR 0.006 0.001 TYR A 303 ARG 0.005 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.59 seconds wall clock time: 57 minutes 8.86 seconds (3428.86 seconds total)