Starting phenix.real_space_refine on Fri May 9 18:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.map" model { file = "/net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0s_63562/05_2025/9m0s_63562.cif" } resolution = 3.5 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= 0.001 sd= 0.046 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 3 5.49 5 S 13 5.16 5 C 2288 2.51 5 N 515 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3413 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3362 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.83 Number of scatterers: 3413 At special positions: 0 Unit cell: (73.87, 68.06, 77.19, 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 13 16.00 P 3 15.00 O 594 8.00 N 515 7.00 C 2288 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: 0.82 Conformation dependent library (CDL) restraints added in 374.5 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 71 through 102 removed outlier: 4.471A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 88 - end of helix Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.972A pdb=" N SER A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 144 through 166 removed outlier: 4.718A pdb=" N ASP A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 removed outlier: 4.283A pdb=" N LEU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.556A pdb=" N SER A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.679A pdb=" N CYS A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 278 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 307 through 321 removed outlier: 4.366A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 4.060A pdb=" N ALA A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLY A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.153A pdb=" N LEU A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 373 through 397 Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 407 through 440 removed outlier: 3.752A pdb=" N TYR A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 470 removed outlier: 4.710A pdb=" N THR A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.511A pdb=" N THR A 475 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 535 removed outlier: 4.078A pdb=" N VAL A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Proline residue: A 530 - end of helix 239 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 505 1.31 - 1.44: 1009 1.44 - 1.57: 1969 1.57 - 1.70: 7 1.70 - 1.83: 22 Bond restraints: 3512 Sorted by residual: bond pdb=" C6A ACO A 601 " pdb=" N6A ACO A 601 " ideal model delta sigma weight residual 1.337 1.478 -0.141 1.00e-02 1.00e+04 1.98e+02 bond pdb=" C5P ACO A 601 " pdb=" N4P ACO A 601 " ideal model delta sigma weight residual 1.331 1.474 -0.143 1.20e-02 6.94e+03 1.42e+02 bond pdb=" C9P ACO A 601 " pdb=" N8P ACO A 601 " ideal model delta sigma weight residual 1.333 1.480 -0.147 1.30e-02 5.92e+03 1.28e+02 bond pdb=" C3B ACO A 601 " pdb=" O3B ACO A 601 " ideal model delta sigma weight residual 1.444 1.338 0.106 1.20e-02 6.94e+03 7.75e+01 bond pdb=" O5B ACO A 601 " pdb=" P1A ACO A 601 " ideal model delta sigma weight residual 1.579 1.674 -0.095 1.50e-02 4.44e+03 4.01e+01 ... (remaining 3507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 4651 2.76 - 5.52: 118 5.52 - 8.28: 31 8.28 - 11.05: 7 11.05 - 13.81: 2 Bond angle restraints: 4809 Sorted by residual: angle pdb=" P1A ACO A 601 " pdb=" O3A ACO A 601 " pdb=" P2A ACO A 601 " ideal model delta sigma weight residual 136.83 123.02 13.81 1.00e+00 1.00e+00 1.91e+02 angle pdb=" N1A ACO A 601 " pdb=" C2A ACO A 601 " pdb=" N3A ACO A 601 " ideal model delta sigma weight residual 128.69 119.81 8.88 1.00e+00 1.00e+00 7.89e+01 angle pdb=" C5A ACO A 601 " pdb=" C4A ACO A 601 " pdb=" N3A ACO A 601 " ideal model delta sigma weight residual 126.80 120.12 6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" C ACO A 601 " pdb=" S1P ACO A 601 " pdb=" C2P ACO A 601 " ideal model delta sigma weight residual 101.25 107.61 -6.36 1.00e+00 1.00e+00 4.05e+01 angle pdb=" CH3 ACO A 601 " pdb=" C ACO A 601 " pdb=" S1P ACO A 601 " ideal model delta sigma weight residual 112.98 119.28 -6.30 1.00e+00 1.00e+00 3.97e+01 ... (remaining 4804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1877 15.87 - 31.74: 96 31.74 - 47.62: 44 47.62 - 63.49: 15 63.49 - 79.36: 3 Dihedral angle restraints: 2035 sinusoidal: 800 harmonic: 1235 Sorted by residual: dihedral pdb=" CA GLU A 338 " pdb=" C GLU A 338 " pdb=" N GLY A 339 " pdb=" CA GLY A 339 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA MET A 307 " pdb=" C MET A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ARG A 246 " pdb=" C ARG A 246 " pdb=" N PHE A 247 " pdb=" CA PHE A 247 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 346 0.048 - 0.096: 136 0.096 - 0.144: 58 0.144 - 0.192: 19 0.192 - 0.240: 6 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB VAL A 353 " pdb=" CA VAL A 353 " pdb=" CG1 VAL A 353 " pdb=" CG2 VAL A 353 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL A 350 " pdb=" CA VAL A 350 " pdb=" CG1 VAL A 350 " pdb=" CG2 VAL A 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 363 " pdb=" CA ILE A 363 " pdb=" CG1 ILE A 363 " pdb=" CG2 ILE A 363 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 562 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 186 " -0.023 2.00e-02 2.50e+03 1.97e-02 6.81e+00 pdb=" CG PHE A 186 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 186 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 186 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 186 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 186 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 186 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 340 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 341 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 149 " 0.015 2.00e-02 2.50e+03 1.59e-02 5.07e+00 pdb=" CG TYR A 149 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 149 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 149 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 149 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 149 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 149 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 149 " -0.000 2.00e-02 2.50e+03 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 925 2.80 - 3.33: 3322 3.33 - 3.85: 5836 3.85 - 4.38: 6658 4.38 - 4.90: 11060 Nonbonded interactions: 27801 Sorted by model distance: nonbonded pdb=" OH TYR A 82 " pdb=" OD1 ASP A 198 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 225 " pdb=" O9A ACO A 601 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLU A 389 " pdb=" OG SER A 417 " model vdw 2.308 3.040 nonbonded pdb=" O PHE A 268 " pdb=" OG1 THR A 272 " model vdw 2.313 3.040 nonbonded pdb=" OG1 THR A 331 " pdb=" OH TYR A 510 " model vdw 2.328 3.040 ... (remaining 27796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.130 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.310 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 0.147 3512 Z= 0.603 Angle : 1.184 13.807 4809 Z= 0.671 Chirality : 0.065 0.240 565 Planarity : 0.009 0.059 574 Dihedral : 13.207 79.361 1243 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -3.69 (0.31), residues: 418 helix: -2.36 (0.21), residues: 316 sheet: None (None), residues: 0 loop : -1.94 (0.55), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 524 HIS 0.002 0.001 HIS A 402 PHE 0.042 0.003 PHE A 186 TYR 0.039 0.003 TYR A 149 ARG 0.005 0.001 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.09968 ( 239) hydrogen bonds : angle 5.98406 ( 714) covalent geometry : bond 0.00969 ( 3512) covalent geometry : angle 1.18402 ( 4809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.325 Fit side-chains REVERT: A 175 ASP cc_start: 0.8680 (t0) cc_final: 0.8091 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1458 time to fit residues: 9.2847 Evaluate side-chains 37 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.157090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125570 restraints weight = 3800.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130253 restraints weight = 2037.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133487 restraints weight = 1379.938| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3512 Z= 0.176 Angle : 0.675 7.976 4809 Z= 0.343 Chirality : 0.043 0.128 565 Planarity : 0.005 0.042 574 Dihedral : 12.229 61.406 503 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.10 % Allowed : 9.59 % Favored : 89.32 % 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: -1.33 (0.38), residues: 418 helix: -0.64 (0.26), residues: 332 sheet: None (None), residues: 0 loop : -1.14 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 143 HIS 0.002 0.001 HIS A 402 PHE 0.025 0.002 PHE A 186 TYR 0.014 0.001 TYR A 149 ARG 0.011 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 239) hydrogen bonds : angle 4.70845 ( 714) covalent geometry : bond 0.00411 ( 3512) covalent geometry : angle 0.67541 ( 4809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.379 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1584 time to fit residues: 8.6786 Evaluate side-chains 38 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.154421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123557 restraints weight = 3858.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128193 restraints weight = 2077.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131350 restraints weight = 1410.372| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3512 Z= 0.177 Angle : 0.651 7.835 4809 Z= 0.329 Chirality : 0.043 0.121 565 Planarity : 0.005 0.037 574 Dihedral : 11.861 60.611 503 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.92 % Allowed : 11.23 % Favored : 86.85 % 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: -0.09 (0.41), residues: 418 helix: 0.15 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -0.34 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 143 HIS 0.002 0.001 HIS A 402 PHE 0.023 0.002 PHE A 186 TYR 0.013 0.001 TYR A 149 ARG 0.003 0.001 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 239) hydrogen bonds : angle 4.47557 ( 714) covalent geometry : bond 0.00418 ( 3512) covalent geometry : angle 0.65145 ( 4809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.325 Fit side-chains REVERT: A 111 PHE cc_start: 0.8120 (t80) cc_final: 0.7845 (t80) REVERT: A 338 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6375 (mt-10) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1519 time to fit residues: 7.9187 Evaluate side-chains 40 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.156133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124034 restraints weight = 3824.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128848 restraints weight = 1991.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132325 restraints weight = 1336.426| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3512 Z= 0.147 Angle : 0.608 7.743 4809 Z= 0.305 Chirality : 0.041 0.117 565 Planarity : 0.004 0.034 574 Dihedral : 11.619 60.353 503 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.19 % Allowed : 13.97 % Favored : 83.84 % 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: 0.43 (0.42), residues: 418 helix: 0.51 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -0.17 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.001 0.001 HIS A 402 PHE 0.020 0.001 PHE A 186 TYR 0.010 0.001 TYR A 149 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 239) hydrogen bonds : angle 4.29805 ( 714) covalent geometry : bond 0.00342 ( 3512) covalent geometry : angle 0.60810 ( 4809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.326 Fit side-chains REVERT: A 205 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7496 (pp) REVERT: A 338 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6505 (mt-10) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1465 time to fit residues: 7.7581 Evaluate side-chains 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.156771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124291 restraints weight = 3879.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129379 restraints weight = 2002.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132739 restraints weight = 1332.753| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3512 Z= 0.141 Angle : 0.598 7.641 4809 Z= 0.299 Chirality : 0.041 0.116 565 Planarity : 0.004 0.033 574 Dihedral : 11.433 59.411 503 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.84 % Allowed : 13.70 % Favored : 82.47 % 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: 0.72 (0.42), residues: 418 helix: 0.74 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.22 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.001 0.001 HIS A 402 PHE 0.019 0.001 PHE A 186 TYR 0.009 0.001 TYR A 149 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 239) hydrogen bonds : angle 4.22277 ( 714) covalent geometry : bond 0.00326 ( 3512) covalent geometry : angle 0.59834 ( 4809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.383 Fit side-chains REVERT: A 205 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7477 (pp) REVERT: A 338 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6570 (mt-10) outliers start: 14 outliers final: 7 residues processed: 48 average time/residue: 0.1277 time to fit residues: 8.2148 Evaluate side-chains 42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.0370 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.176120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149747 restraints weight = 3675.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153881 restraints weight = 2139.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156690 restraints weight = 1535.759| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3512 Z= 0.131 Angle : 0.597 7.844 4809 Z= 0.297 Chirality : 0.041 0.127 565 Planarity : 0.004 0.034 574 Dihedral : 11.258 58.151 503 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 16.16 % Favored : 81.37 % 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: 0.90 (0.43), residues: 418 helix: 0.85 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.10 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 143 HIS 0.001 0.000 HIS A 402 PHE 0.017 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 239) hydrogen bonds : angle 4.16547 ( 714) covalent geometry : bond 0.00297 ( 3512) covalent geometry : angle 0.59706 ( 4809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.355 Fit side-chains REVERT: A 205 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7526 (pp) REVERT: A 338 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6661 (mt-10) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.1334 time to fit residues: 6.8770 Evaluate side-chains 40 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3685 r_free = 0.3685 target = 0.155568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123756 restraints weight = 3853.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128452 restraints weight = 2128.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131575 restraints weight = 1472.552| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3512 Z= 0.155 Angle : 0.613 7.857 4809 Z= 0.305 Chirality : 0.042 0.125 565 Planarity : 0.004 0.035 574 Dihedral : 11.268 56.613 503 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.84 % Allowed : 15.34 % Favored : 80.82 % 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: 0.95 (0.43), residues: 418 helix: 0.87 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.04 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 143 HIS 0.002 0.001 HIS A 402 PHE 0.017 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 239) hydrogen bonds : angle 4.22429 ( 714) covalent geometry : bond 0.00370 ( 3512) covalent geometry : angle 0.61274 ( 4809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.323 Fit side-chains REVERT: A 205 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7468 (pp) REVERT: A 254 ILE cc_start: 0.7933 (mm) cc_final: 0.7630 (mp) REVERT: A 338 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6580 (mt-10) outliers start: 14 outliers final: 9 residues processed: 43 average time/residue: 0.1307 time to fit residues: 7.4428 Evaluate side-chains 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125820 restraints weight = 3829.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130654 restraints weight = 2100.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133755 restraints weight = 1446.184| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3512 Z= 0.135 Angle : 0.597 7.836 4809 Z= 0.297 Chirality : 0.041 0.126 565 Planarity : 0.004 0.035 574 Dihedral : 11.047 57.494 503 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.56 % Allowed : 15.62 % Favored : 80.82 % 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: 1.06 (0.43), residues: 418 helix: 0.94 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.12 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 143 HIS 0.001 0.001 HIS A 402 PHE 0.016 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 239) hydrogen bonds : angle 4.16494 ( 714) covalent geometry : bond 0.00312 ( 3512) covalent geometry : angle 0.59732 ( 4809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.358 Fit side-chains REVERT: A 254 ILE cc_start: 0.7884 (mm) cc_final: 0.7619 (mp) REVERT: A 338 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6612 (mt-10) outliers start: 13 outliers final: 9 residues processed: 40 average time/residue: 0.1209 time to fit residues: 6.5957 Evaluate side-chains 39 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 10 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126330 restraints weight = 3753.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131298 restraints weight = 2035.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134650 restraints weight = 1386.246| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3512 Z= 0.131 Angle : 0.588 7.829 4809 Z= 0.292 Chirality : 0.041 0.127 565 Planarity : 0.004 0.036 574 Dihedral : 10.578 50.435 503 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.01 % Allowed : 15.89 % Favored : 81.10 % 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: 1.26 (0.43), residues: 418 helix: 1.07 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.23 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 143 HIS 0.001 0.000 HIS A 402 PHE 0.015 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 239) hydrogen bonds : angle 4.11541 ( 714) covalent geometry : bond 0.00303 ( 3512) covalent geometry : angle 0.58798 ( 4809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.298 Fit side-chains REVERT: A 338 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6567 (mt-10) outliers start: 11 outliers final: 7 residues processed: 37 average time/residue: 0.1188 time to fit residues: 6.0742 Evaluate side-chains 37 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.159052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127171 restraints weight = 3816.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131981 restraints weight = 2110.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135086 restraints weight = 1449.724| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3512 Z= 0.132 Angle : 0.586 7.829 4809 Z= 0.292 Chirality : 0.041 0.124 565 Planarity : 0.004 0.036 574 Dihedral : 10.175 46.866 503 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 16.44 % Favored : 81.10 % 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: 1.33 (0.43), residues: 418 helix: 1.10 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.34 (0.79), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 524 HIS 0.001 0.000 HIS A 402 PHE 0.015 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 239) hydrogen bonds : angle 4.08883 ( 714) covalent geometry : bond 0.00304 ( 3512) covalent geometry : angle 0.58569 ( 4809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.351 Fit side-chains REVERT: A 338 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6636 (mt-10) outliers start: 9 outliers final: 6 residues processed: 34 average time/residue: 0.1272 time to fit residues: 5.8022 Evaluate side-chains 34 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.158305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126534 restraints weight = 3806.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131255 restraints weight = 2116.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134484 restraints weight = 1462.548| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3512 Z= 0.140 Angle : 0.595 7.835 4809 Z= 0.297 Chirality : 0.041 0.125 565 Planarity : 0.004 0.036 574 Dihedral : 9.889 44.966 503 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.74 % Allowed : 16.44 % Favored : 80.82 % 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: 1.32 (0.43), residues: 418 helix: 1.08 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.37 (0.79), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 524 HIS 0.001 0.001 HIS A 402 PHE 0.015 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 239) hydrogen bonds : angle 4.11449 ( 714) covalent geometry : bond 0.00328 ( 3512) covalent geometry : angle 0.59534 ( 4809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1431.94 seconds wall clock time: 25 minutes 46.63 seconds (1546.63 seconds total)