Starting phenix.real_space_refine on Sat Apr 26 20:47:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0s_63562/04_2025/9m0s_63562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0s_63562/04_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_63562/04_2025/9m0s_63562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0s_63562/04_2025/9m0s_63562.map" model { file = "/net/cci-nas-00/data/ceres_data/9m0s_63562/04_2025/9m0s_63562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0s_63562/04_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-5669/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: 2.95, per 1000 atoms: 0.86 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: 0.99 Conformation dependent library (CDL) restraints added in 462.1 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: 0.34 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: 0.95 Time building geometry restraints manager: 1.00 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: 1.270 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: 0.030 Process input model: 13.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- 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 : 0.355 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: 0.1629 time to fit residues: 10.2231 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 : 0.329 ------------------------------------------------------------------------------- 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 = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125547 restraints weight = 3800.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130265 restraints weight = 2040.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133483 restraints weight = 1380.989| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 4.70844 ( 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 : 0.344 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1564 time to fit residues: 8.5842 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.7980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 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: 0.6980 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125668 restraints weight = 3828.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130301 restraints weight = 2033.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133605 restraints weight = 1367.622| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3512 Z= 0.160 Angle : 0.636 7.869 4809 Z= 0.320 Chirality : 0.042 0.119 565 Planarity : 0.005 0.037 574 Dihedral : 11.842 60.394 503 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 11.23 % Favored : 86.58 % 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: -0.16 (0.41), residues: 418 helix: 0.11 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.46 (0.69), residues: 84 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 0.022 0.002 PHE A 186 TYR 0.012 0.001 TYR A 149 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 239) hydrogen bonds : angle 4.45473 ( 714) covalent geometry : bond 0.00374 ( 3512) covalent geometry : angle 0.63593 ( 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: 8 poor density : 34 time to evaluate : 0.354 Fit side-chains REVERT: A 338 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6304 (mt-10) outliers start: 8 outliers final: 4 residues processed: 40 average time/residue: 0.1703 time to fit residues: 8.5314 Evaluate side-chains 40 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN 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: 3.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.156734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124895 restraints weight = 3815.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129663 restraints weight = 2040.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132959 restraints weight = 1378.950| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3512 Z= 0.150 Angle : 0.615 7.787 4809 Z= 0.310 Chirality : 0.041 0.120 565 Planarity : 0.005 0.036 574 Dihedral : 11.710 60.369 503 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 12.05 % Favored : 85.75 % 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: 0.31 (0.42), residues: 418 helix: 0.43 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -0.21 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 264 HIS 0.002 0.001 HIS A 402 PHE 0.021 0.001 PHE A 186 TYR 0.009 0.001 TYR A 149 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 239) hydrogen bonds : angle 4.36982 ( 714) covalent geometry : bond 0.00348 ( 3512) covalent geometry : angle 0.61513 ( 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 : 0.328 Fit side-chains REVERT: A 205 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7536 (pp) REVERT: A 338 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6356 (mt-10) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.1490 time to fit residues: 7.6018 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN 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: 0.8980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.157495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125402 restraints weight = 3882.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130206 restraints weight = 2080.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133618 restraints weight = 1398.849| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3512 Z= 0.137 Angle : 0.603 7.697 4809 Z= 0.303 Chirality : 0.041 0.116 565 Planarity : 0.004 0.035 574 Dihedral : 11.558 59.936 503 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.74 % Allowed : 12.88 % Favored : 84.38 % 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: 0.61 (0.42), residues: 418 helix: 0.64 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -0.12 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.001 0.001 HIS A 402 PHE 0.019 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 0.03613 ( 239) hydrogen bonds : angle 4.31018 ( 714) covalent geometry : bond 0.00311 ( 3512) covalent geometry : angle 0.60260 ( 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 45 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.355 Fit side-chains REVERT: A 205 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7481 (pp) REVERT: A 254 ILE cc_start: 0.7892 (mm) cc_final: 0.7491 (mp) REVERT: A 338 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6398 (mt-10) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.1472 time to fit residues: 7.9478 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 : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.0050 chunk 7 optimal weight: 0.0670 chunk 29 optimal weight: 0.5980 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127142 restraints weight = 3808.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132183 restraints weight = 1975.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135452 restraints weight = 1315.415| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3512 Z= 0.123 Angle : 0.590 7.846 4809 Z= 0.297 Chirality : 0.040 0.122 565 Planarity : 0.004 0.033 574 Dihedral : 11.369 59.094 503 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.82 (0.42), residues: 418 helix: 0.80 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.12 (0.74), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.001 0.000 HIS A 402 PHE 0.018 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 239) hydrogen bonds : angle 4.23248 ( 714) covalent geometry : bond 0.00267 ( 3512) covalent geometry : angle 0.59002 ( 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 47 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.526 Fit side-chains REVERT: A 205 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7533 (pp) REVERT: A 338 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6578 (mt-10) outliers start: 14 outliers final: 8 residues processed: 44 average time/residue: 0.1270 time to fit residues: 7.5171 Evaluate side-chains 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 26 optimal weight: 0.2980 chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.159413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126689 restraints weight = 3785.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131759 restraints weight = 1976.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135257 restraints weight = 1320.763| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3512 Z= 0.134 Angle : 0.599 7.831 4809 Z= 0.299 Chirality : 0.042 0.125 565 Planarity : 0.004 0.033 574 Dihedral : 11.303 58.405 503 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.74 % Allowed : 14.52 % Favored : 82.74 % 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: 0.86 (0.42), residues: 418 helix: 0.84 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.001 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 246 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 239) hydrogen bonds : angle 4.22007 ( 714) covalent geometry : bond 0.00308 ( 3512) covalent geometry : angle 0.59905 ( 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 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.362 Fit side-chains REVERT: A 205 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7415 (pp) REVERT: A 338 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6532 (mt-10) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.1295 time to fit residues: 7.1562 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 : 0.370 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.160828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128012 restraints weight = 3790.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133190 restraints weight = 1973.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136483 restraints weight = 1318.938| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 0.033 3512 Z= 0.124 Angle : 0.591 7.818 4809 Z= 0.295 Chirality : 0.041 0.118 565 Planarity : 0.004 0.034 574 Dihedral : 11.161 57.152 503 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.74 % Allowed : 15.62 % Favored : 81.64 % 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: 0.98 (0.43), residues: 418 helix: 0.91 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.09 (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 0.016 0.001 PHE A 186 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 239) hydrogen bonds : angle 4.17948 ( 714) covalent geometry : bond 0.00274 ( 3512) covalent geometry : angle 0.59089 ( 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: 10 poor density : 32 time to evaluate : 0.327 Fit side-chains REVERT: A 185 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5070 (mp) REVERT: A 205 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7340 (pp) REVERT: A 338 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6457 (mt-10) outliers start: 10 outliers final: 7 residues processed: 40 average time/residue: 0.1323 time to fit residues: 7.0727 Evaluate side-chains 42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 185 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.158451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126323 restraints weight = 3743.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131320 restraints weight = 1966.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134767 restraints weight = 1315.236| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2460 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 : 0.602 7.831 4809 Z= 0.300 Chirality : 0.041 0.118 565 Planarity : 0.004 0.034 574 Dihedral : 11.132 56.086 503 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.74 % Allowed : 15.34 % Favored : 81.92 % 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: 1.01 (0.43), residues: 418 helix: 0.92 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -0.00 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 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 0.03448 ( 239) hydrogen bonds : angle 4.20062 ( 714) covalent geometry : bond 0.00329 ( 3512) covalent geometry : angle 0.60163 ( 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 43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.363 Fit side-chains REVERT: A 205 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7297 (pp) REVERT: A 254 ILE cc_start: 0.7924 (mm) cc_final: 0.7608 (mp) REVERT: A 338 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6570 (mt-10) outliers start: 10 outliers final: 6 residues processed: 41 average time/residue: 0.1328 time to fit residues: 7.2227 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 : 0.360 ------------------------------------------------------------------------------- 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 205 LEU 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 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 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 = 0.3708 r_free = 0.3708 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124960 restraints weight = 3812.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129957 restraints weight = 2021.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133431 restraints weight = 1368.140| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3512 Z= 0.153 Angle : 0.612 8.092 4809 Z= 0.305 Chirality : 0.042 0.120 565 Planarity : 0.004 0.034 574 Dihedral : 11.117 55.048 503 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 15.62 % Favored : 82.19 % 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: 1.04 (0.43), residues: 418 helix: 0.93 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.06 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.002 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 0.03510 ( 239) hydrogen bonds : angle 4.23469 ( 714) covalent geometry : bond 0.00362 ( 3512) covalent geometry : angle 0.61182 ( 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 41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.315 Fit side-chains REVERT: A 205 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7322 (pp) REVERT: A 254 ILE cc_start: 0.7959 (mm) cc_final: 0.7645 (mp) REVERT: A 338 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6607 (mt-10) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1295 time to fit residues: 6.6961 Evaluate side-chains 41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 205 LEU 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: 0.6980 chunk 18 optimal weight: 0.0170 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.0000 overall best weight: 0.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131119 restraints weight = 3767.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136031 restraints weight = 2071.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139353 restraints weight = 1418.661| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3512 Z= 0.118 Angle : 0.578 7.794 4809 Z= 0.288 Chirality : 0.040 0.131 565 Planarity : 0.004 0.034 574 Dihedral : 10.616 57.058 503 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 15.62 % Favored : 82.19 % 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: 1.08 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.16 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 462 HIS 0.001 0.000 HIS A 402 PHE 0.014 0.001 PHE A 186 TYR 0.008 0.001 TYR A 409 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 239) hydrogen bonds : angle 4.07129 ( 714) covalent geometry : bond 0.00254 ( 3512) covalent geometry : angle 0.57797 ( 4809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.42 seconds wall clock time: 26 minutes 55.37 seconds (1615.37 seconds total)