Starting phenix.real_space_refine on Tue Feb 11 00:12:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m7d_30129/02_2025/6m7d_30129.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m7d_30129/02_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_30129/02_2025/6m7d_30129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m7d_30129/02_2025/6m7d_30129.map" model { file = "/net/cci-nas-00/data/ceres_data/6m7d_30129/02_2025/6m7d_30129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m7d_30129/02_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-5592/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: 4.70, per 1000 atoms: 1.43 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: 0.77 Conformation dependent library (CDL) restraints added in 305.7 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: 1.05 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: 0.70 Time building geometry restraints manager: 0.81 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: 8.600 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.590 Find NCS groups from input model: 0.030 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- 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 : 0.332 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: 1.4279 time to fit residues: 99.4887 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 : 0.370 ------------------------------------------------------------------------------- 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 = 0.123926 restraints weight = 3449.531| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.02 r_work: 0.2933 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 : 9.681 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 : 0.353 Fit side-chains REVERT: A 56 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 62 LEU cc_start: 0.9079 (mt) cc_final: 0.8831 (mm) REVERT: A 290 ARG cc_start: 0.8697 (ttt180) cc_final: 0.7612 (ttp-110) REVERT: A 345 LYS cc_start: 0.8293 (tppt) cc_final: 0.8028 (mmpt) REVERT: A 377 SER cc_start: 0.8852 (p) cc_final: 0.8592 (p) REVERT: A 400 ASN cc_start: 0.8235 (m-40) cc_final: 0.8012 (m-40) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 1.2739 time to fit residues: 76.0171 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 : 0.372 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 0.0050 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.146749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.122715 restraints weight = 3337.475| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.11 r_work: 0.2902 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2409 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= 0.171 Angle : 0.456 4.903 4556 Z= 0.243 Chirality : 0.039 0.116 533 Planarity : 0.003 0.031 564 Dihedral : 9.655 59.816 541 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 1.56 (0.40), residues: 410 helix: 1.30 (0.34), residues: 242 sheet: -0.35 (0.92), residues: 25 loop : 1.12 (0.49), residues: 143 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 0.012 0.001 PHE A 269 TYR 0.006 0.001 TYR A 275 ARG 0.002 0.000 ARG A 395 *********************** 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 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.380 Fit side-chains REVERT: A 56 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8387 (p) REVERT: A 290 ARG cc_start: 0.8747 (ttt180) cc_final: 0.7626 (ttp-110) REVERT: A 345 LYS cc_start: 0.8256 (tppt) cc_final: 0.8028 (mmpt) REVERT: A 377 SER cc_start: 0.8870 (p) cc_final: 0.8602 (p) REVERT: A 400 ASN cc_start: 0.8241 (m-40) cc_final: 0.7999 (m-40) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 1.3092 time to fit residues: 70.0225 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.123755 restraints weight = 3442.720| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.12 r_work: 0.2851 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2597 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= 0.158 Angle : 0.442 5.237 4556 Z= 0.235 Chirality : 0.039 0.118 533 Planarity : 0.003 0.030 564 Dihedral : 9.573 59.732 541 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.08 % Allowed : 13.70 % 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: 1.75 (0.41), residues: 410 helix: 1.46 (0.34), residues: 242 sheet: -0.40 (0.88), residues: 25 loop : 1.21 (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 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.341 Fit side-chains REVERT: A 56 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 201 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5802 (tt0) REVERT: A 290 ARG cc_start: 0.8663 (ttt180) cc_final: 0.7592 (ttp-110) REVERT: A 345 LYS cc_start: 0.8193 (tppt) cc_final: 0.7987 (mmpt) REVERT: A 377 SER cc_start: 0.8840 (p) cc_final: 0.8583 (p) REVERT: A 400 ASN cc_start: 0.8158 (m-40) cc_final: 0.7905 (m-40) outliers start: 14 outliers final: 7 residues processed: 60 average time/residue: 1.2665 time to fit residues: 78.2241 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 84 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.152031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.129118 restraints weight = 3449.520| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.93 r_work: 0.2975 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2980 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= 0.126 Angle : 0.425 5.766 4556 Z= 0.225 Chirality : 0.038 0.120 533 Planarity : 0.003 0.030 564 Dihedral : 9.513 59.495 541 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.33 % Allowed : 15.45 % 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: 2.02 (0.41), residues: 410 helix: 1.72 (0.34), residues: 243 sheet: -0.30 (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 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.388 Fit side-chains REVERT: A 125 MET cc_start: 0.7064 (tpt) cc_final: 0.6828 (tpt) REVERT: A 201 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5753 (tt0) REVERT: A 290 ARG cc_start: 0.8524 (ttt180) cc_final: 0.7567 (ttp-110) REVERT: A 377 SER cc_start: 0.8751 (p) cc_final: 0.8520 (p) REVERT: A 400 ASN cc_start: 0.8076 (m-40) cc_final: 0.7854 (m-40) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 1.1166 time to fit residues: 68.1718 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.146829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.123048 restraints weight = 3455.357| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.05 r_work: 0.2875 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3348 Z= 0.195 Angle : 0.479 8.363 4556 Z= 0.246 Chirality : 0.040 0.153 533 Planarity : 0.003 0.029 564 Dihedral : 9.512 59.779 541 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.92 % Allowed : 15.45 % 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: 1.98 (0.41), residues: 410 helix: 1.58 (0.34), residues: 242 sheet: -0.16 (0.90), residues: 25 loop : 1.41 (0.50), 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 397 PHE 0.009 0.001 PHE A 269 TYR 0.006 0.001 TYR A 303 ARG 0.004 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 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.307 Fit side-chains REVERT: A 201 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.5867 (tt0) REVERT: A 290 ARG cc_start: 0.8618 (ttt180) cc_final: 0.7627 (ttp-110) REVERT: A 400 ASN cc_start: 0.8194 (m-40) cc_final: 0.7923 (m-40) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.0982 time to fit residues: 59.0663 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 90 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.145899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.122071 restraints weight = 3418.383| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.04 r_work: 0.2853 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3348 Z= 0.207 Angle : 0.484 7.009 4556 Z= 0.250 Chirality : 0.041 0.138 533 Planarity : 0.003 0.029 564 Dihedral : 9.548 59.851 541 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.62 % Allowed : 16.33 % Favored : 81.05 % 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: 1.94 (0.41), residues: 410 helix: 1.55 (0.35), residues: 240 sheet: 0.19 (0.93), residues: 25 loop : 1.32 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 PHE 0.009 0.001 PHE A 269 TYR 0.009 0.001 TYR A 127 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 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.341 Fit side-chains REVERT: A 201 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5963 (tt0) REVERT: A 290 ARG cc_start: 0.8654 (ttt180) cc_final: 0.7625 (ttp-110) REVERT: A 400 ASN cc_start: 0.8200 (m-40) cc_final: 0.7932 (m-40) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.2662 time to fit residues: 66.5223 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 90 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.148246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.125341 restraints weight = 3417.432| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.01 r_work: 0.2953 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3348 Z= 0.154 Angle : 0.464 7.319 4556 Z= 0.238 Chirality : 0.039 0.126 533 Planarity : 0.003 0.029 564 Dihedral : 9.493 59.743 541 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.67 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: 2.05 (0.41), residues: 410 helix: 1.61 (0.34), residues: 242 sheet: 0.32 (0.91), residues: 25 loop : 1.39 (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 0.006 0.001 TYR A 303 ARG 0.005 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 : 0.404 Fit side-chains REVERT: A 201 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5817 (tt0) REVERT: A 290 ARG cc_start: 0.8747 (ttt180) cc_final: 0.7636 (ttp-110) REVERT: A 400 ASN cc_start: 0.8235 (m-40) cc_final: 0.7968 (m-40) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 1.1946 time to fit residues: 60.4350 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 90 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 39 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: ** 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 = 0.3512 r_free = 0.3512 target = 0.147184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.123009 restraints weight = 3426.180| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.03 r_work: 0.2923 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2870 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= 0.175 Angle : 0.478 7.513 4556 Z= 0.246 Chirality : 0.040 0.125 533 Planarity : 0.003 0.029 564 Dihedral : 9.493 59.768 541 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % 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: 2.05 (0.41), residues: 410 helix: 1.56 (0.34), residues: 242 sheet: 0.43 (0.92), residues: 25 loop : 1.47 (0.52), 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 0.012 0.001 PHE A 269 TYR 0.011 0.001 TYR A 127 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 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.343 Fit side-chains REVERT: A 201 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.5848 (tt0) REVERT: A 290 ARG cc_start: 0.8747 (ttt180) cc_final: 0.7629 (ttp-110) REVERT: A 400 ASN cc_start: 0.8233 (m-40) cc_final: 0.7941 (m-40) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 1.2113 time to fit residues: 58.7829 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 90 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 40 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.147969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.123694 restraints weight = 3349.767| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.90 r_work: 0.2967 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2896 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= 0.167 Angle : 0.482 7.742 4556 Z= 0.246 Chirality : 0.039 0.123 533 Planarity : 0.003 0.030 564 Dihedral : 9.482 59.758 541 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % 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: 1.57 (0.34), residues: 242 sheet: 0.39 (0.91), residues: 25 loop : 1.48 (0.52), 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 0.012 0.001 PHE A 269 TYR 0.006 0.001 TYR A 303 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 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.342 Fit side-chains REVERT: A 201 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5809 (tt0) REVERT: A 290 ARG cc_start: 0.8704 (ttt180) cc_final: 0.7611 (ttp-110) REVERT: A 400 ASN cc_start: 0.8204 (m-40) cc_final: 0.7941 (m-40) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 1.2258 time to fit residues: 59.4452 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 90 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.150399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.126290 restraints weight = 3425.514| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.96 r_work: 0.2998 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3129 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= 0.141 Angle : 0.464 7.736 4556 Z= 0.237 Chirality : 0.039 0.119 533 Planarity : 0.003 0.030 564 Dihedral : 9.437 59.633 541 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.04 % Allowed : 16.62 % 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: 2.17 (0.41), residues: 410 helix: 1.70 (0.34), residues: 242 sheet: 0.43 (0.92), residues: 25 loop : 1.43 (0.52), 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 0.014 0.001 PHE A 269 TYR 0.013 0.001 TYR A 127 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: 3292.94 seconds wall clock time: 59 minutes 22.28 seconds (3562.28 seconds total)