Starting phenix.real_space_refine on Wed Mar 5 18:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403.map" model { file = "/net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9je0_61403/03_2025/9je0_61403_neut.cif" } resolution = 3.23 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= 0.004 sd= 0.071 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 Br 2 7.06 5 S 28 5.16 5 C 2176 2.51 5 N 554 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 26, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.59, per 1000 atoms: 0.78 Number of scatterers: 3321 At special positions: 0 Unit cell: (94.9, 52.56, 66.43, 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) Br 2 34.99 S 28 16.00 O 561 8.00 N 554 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 386.7 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 83.0% alpha, 1.4% 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 20 through 42 removed outlier: 4.208A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.765A pdb=" N ASN A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.571A pdb=" N LEU A 98 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.548A pdb=" N HIS A 142 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.261A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.530A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 4.311A pdb=" N GLU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 255 Processing helix chain 'A' and resid 257 through 273 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 339 through 343 removed outlier: 4.040A pdb=" N ARG A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.600A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix removed outlier: 4.161A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.005A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 465 No H-bonds generated for 'chain 'A' and resid 464 through 465' Processing helix chain 'A' and resid 467 through 467 No H-bonds generated for 'chain 'A' and resid 467 through 467' Processing helix chain 'A' and resid 468 through 487 Proline residue: A 484 - end of helix removed outlier: 3.732A pdb=" N ARG A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.682A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.645A pdb=" N ARG A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 690 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: 0.87 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 934 1.34 - 1.49: 1009 1.49 - 1.64: 1419 1.64 - 1.79: 0 1.79 - 1.94: 46 Bond restraints: 3408 Sorted by residual: bond pdb=" CAC R75 A 601 " pdb=" OAG R75 A 601 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" CAB R75 A 601 " pdb="BR2 R75 A 601 " ideal model delta sigma weight residual 1.880 1.940 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" CAD R75 A 601 " pdb="BR1 R75 A 601 " ideal model delta sigma weight residual 1.884 1.940 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " ideal model delta sigma weight residual 1.483 1.528 -0.045 2.00e-02 2.50e+03 4.96e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4591 1.96 - 3.93: 47 3.93 - 5.89: 13 5.89 - 7.85: 2 7.85 - 9.82: 1 Bond angle restraints: 4654 Sorted by residual: angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " ideal model delta sigma weight residual 132.81 126.27 6.54 3.00e+00 1.11e-01 4.75e+00 angle pdb=" C HIS A 245 " pdb=" N GLY A 246 " pdb=" CA GLY A 246 " ideal model delta sigma weight residual 119.94 122.23 -2.29 1.11e+00 8.12e-01 4.26e+00 angle pdb=" CA LEU A 37 " pdb=" CB LEU A 37 " pdb=" CG LEU A 37 " ideal model delta sigma weight residual 116.30 122.73 -6.43 3.50e+00 8.16e-02 3.37e+00 angle pdb=" CAD R75 A 601 " pdb=" CAC R75 A 601 " pdb=" OAG R75 A 601 " ideal model delta sigma weight residual 125.05 119.82 5.23 3.00e+00 1.11e-01 3.03e+00 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 1828 20.98 - 41.95: 123 41.95 - 62.93: 17 62.93 - 83.90: 4 83.90 - 104.88: 2 Dihedral angle restraints: 1974 sinusoidal: 738 harmonic: 1236 Sorted by residual: dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual 263.96 159.08 104.88 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -114.54 28.54 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 118 " pdb=" CB ASP A 118 " pdb=" CG ASP A 118 " pdb=" OD1 ASP A 118 " ideal model delta sinusoidal sigma weight residual -30.00 -84.71 54.71 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 314 0.023 - 0.046: 133 0.046 - 0.070: 62 0.070 - 0.093: 25 0.093 - 0.116: 10 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" C PRO A 115 " pdb=" CB PRO A 115 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.49e-01 ... (remaining 541 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 268 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 44 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 45 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 483 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.72e-01 pdb=" N PRO A 484 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 484 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 484 " -0.013 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 916 2.80 - 3.33: 3286 3.33 - 3.85: 5702 3.85 - 4.38: 6346 4.38 - 4.90: 10742 Nonbonded interactions: 26992 Sorted by model distance: nonbonded pdb=" OG SER A 27 " pdb=" OH TYR A 180 " model vdw 2.281 3.040 nonbonded pdb=" O VAL A 504 " pdb=" OG SER A 508 " model vdw 2.332 3.040 nonbonded pdb=" O TRP A 50 " pdb=" NH1 ARG A 90 " model vdw 2.371 3.120 nonbonded pdb=" OG1 THR A 339 " pdb=" OG1 THR A 467 " model vdw 2.375 3.040 nonbonded pdb=" N GLY A 80 " pdb=" O ARG A 84 " model vdw 2.387 3.120 ... (remaining 26987 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.350 Find NCS groups from input model: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 : 0.003 0.073 3408 Z= 0.219 Angle : 0.579 9.815 4654 Z= 0.294 Chirality : 0.035 0.116 544 Planarity : 0.004 0.030 574 Dihedral : 14.224 104.881 1170 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.61 % Allowed : 8.70 % Favored : 88.70 % 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: -0.32 (0.40), residues: 425 helix: 0.19 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -0.85 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 224 HIS 0.004 0.001 HIS A 245 PHE 0.009 0.001 PHE A 358 TYR 0.004 0.001 TYR A 455 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7798 (ttp) cc_final: 0.7577 (ttm) REVERT: A 169 ARG cc_start: 0.6394 (mmm-85) cc_final: 0.6139 (mtt90) REVERT: A 222 MET cc_start: 0.5510 (ppp) cc_final: 0.4780 (mtm) REVERT: A 270 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.4744 (m-80) REVERT: A 474 MET cc_start: 0.5866 (tpp) cc_final: 0.5478 (mmt) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.1491 time to fit residues: 18.7970 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 270 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 216 ASN ** 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 = 0.4786 r_free = 0.4786 target = 0.246027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.210649 restraints weight = 3611.725| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 2.90 r_work: 0.4368 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3408 Z= 0.202 Angle : 0.601 5.936 4654 Z= 0.285 Chirality : 0.039 0.110 544 Planarity : 0.004 0.030 574 Dihedral : 6.771 84.539 468 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.19 % Allowed : 18.55 % Favored : 78.26 % 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: 1.07 (0.42), residues: 425 helix: 1.09 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.02 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 47 PHE 0.024 0.002 PHE A 362 TYR 0.014 0.001 TYR A 122 ARG 0.003 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7924 (ttp) cc_final: 0.7716 (ttm) REVERT: A 82 ASN cc_start: 0.6179 (m-40) cc_final: 0.5836 (p0) REVERT: A 118 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6843 (t0) REVERT: A 149 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: A 169 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6579 (mtt90) REVERT: A 222 MET cc_start: 0.5215 (ppp) cc_final: 0.4408 (mtm) REVERT: A 270 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.5132 (m-10) REVERT: A 342 ARG cc_start: 0.6471 (ptt90) cc_final: 0.4458 (ptt90) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 0.1207 time to fit residues: 12.7070 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.241880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.206400 restraints weight = 3660.056| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 2.90 r_work: 0.4341 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3408 Z= 0.180 Angle : 0.563 6.101 4654 Z= 0.269 Chirality : 0.038 0.118 544 Planarity : 0.004 0.029 574 Dihedral : 5.723 67.777 467 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.77 % Allowed : 18.55 % Favored : 77.68 % 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: 1.59 (0.43), residues: 425 helix: 1.43 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.32 (0.63), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.002 0.000 HIS A 47 PHE 0.015 0.001 PHE A 362 TYR 0.012 0.001 TYR A 122 ARG 0.005 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7997 (ttp) cc_final: 0.7782 (ttm) REVERT: A 82 ASN cc_start: 0.6188 (m-40) cc_final: 0.5759 (p0) REVERT: A 149 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: A 169 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6520 (mtt180) REVERT: A 186 MET cc_start: 0.7981 (mmm) cc_final: 0.7640 (mmp) REVERT: A 222 MET cc_start: 0.5229 (ppp) cc_final: 0.4495 (mtp) REVERT: A 243 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: A 270 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.5065 (m-80) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.1181 time to fit residues: 12.8431 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.0070 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS A 149 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.238831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.202962 restraints weight = 3730.553| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.94 r_work: 0.4305 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3408 Z= 0.179 Angle : 0.567 6.173 4654 Z= 0.271 Chirality : 0.039 0.121 544 Planarity : 0.004 0.032 574 Dihedral : 4.981 43.445 466 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.32 % Allowed : 20.87 % Favored : 76.81 % 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: 1.86 (0.43), residues: 425 helix: 1.61 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.51 (0.64), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 495 HIS 0.001 0.000 HIS A 245 PHE 0.012 0.001 PHE A 362 TYR 0.010 0.001 TYR A 122 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8060 (ttp) cc_final: 0.7858 (ttm) REVERT: A 82 ASN cc_start: 0.6223 (m-40) cc_final: 0.5542 (t0) REVERT: A 149 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: A 169 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.6654 (mtt90) REVERT: A 186 MET cc_start: 0.7925 (mmm) cc_final: 0.7650 (mmp) REVERT: A 222 MET cc_start: 0.5327 (ppp) cc_final: 0.4562 (mtm) REVERT: A 270 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.5113 (m-80) REVERT: A 394 MET cc_start: 0.6422 (tmm) cc_final: 0.5629 (tmm) REVERT: A 474 MET cc_start: 0.5807 (mmp) cc_final: 0.5385 (mmp) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.1134 time to fit residues: 11.4024 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 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 149 GLN ** A 216 ASN ** 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 = 0.4729 r_free = 0.4729 target = 0.237315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.200927 restraints weight = 3769.119| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.97 r_work: 0.4284 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3408 Z= 0.179 Angle : 0.572 7.082 4654 Z= 0.273 Chirality : 0.039 0.120 544 Planarity : 0.004 0.031 574 Dihedral : 4.757 43.455 465 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.90 % Allowed : 23.19 % Favored : 73.91 % 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: 1.93 (0.43), residues: 425 helix: 1.64 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.58 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.011 0.001 PHE A 362 TYR 0.008 0.001 TYR A 122 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.333 Fit side-chains REVERT: A 29 MET cc_start: 0.8171 (ttp) cc_final: 0.7932 (ttm) REVERT: A 38 GLU cc_start: 0.7615 (tp30) cc_final: 0.7348 (tp30) REVERT: A 56 ASN cc_start: 0.7327 (t0) cc_final: 0.6953 (t0) REVERT: A 149 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: A 169 ARG cc_start: 0.7451 (mmm-85) cc_final: 0.6676 (mtt90) REVERT: A 186 MET cc_start: 0.7945 (mmm) cc_final: 0.7705 (mmp) REVERT: A 222 MET cc_start: 0.5410 (ppp) cc_final: 0.4601 (mtm) REVERT: A 270 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: A 394 MET cc_start: 0.6431 (tmm) cc_final: 0.5613 (tmm) REVERT: A 474 MET cc_start: 0.5947 (mmp) cc_final: 0.5447 (mmp) REVERT: A 499 LEU cc_start: 0.7307 (tt) cc_final: 0.6980 (tp) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.1204 time to fit residues: 12.0941 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.0040 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN A 245 HIS A 382 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.238210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.201428 restraints weight = 3853.855| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 3.04 r_work: 0.4282 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3408 Z= 0.171 Angle : 0.570 7.356 4654 Z= 0.270 Chirality : 0.038 0.120 544 Planarity : 0.004 0.031 574 Dihedral : 4.702 46.635 465 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.77 % Allowed : 21.45 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.43), residues: 425 helix: 1.68 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.68 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.010 0.001 PHE A 362 TYR 0.006 0.001 TYR A 152 ARG 0.001 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.369 Fit side-chains REVERT: A 29 MET cc_start: 0.8216 (ttp) cc_final: 0.7994 (ttm) REVERT: A 36 MET cc_start: 0.7554 (mmt) cc_final: 0.7122 (tpp) REVERT: A 38 GLU cc_start: 0.7626 (tp30) cc_final: 0.7337 (tp30) REVERT: A 56 ASN cc_start: 0.7349 (t0) cc_final: 0.6943 (t0) REVERT: A 149 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7057 (mt0) REVERT: A 169 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6730 (mtt90) REVERT: A 186 MET cc_start: 0.7836 (mmm) cc_final: 0.7630 (mmp) REVERT: A 222 MET cc_start: 0.5389 (ppp) cc_final: 0.4594 (mtm) REVERT: A 270 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: A 474 MET cc_start: 0.5865 (mmp) cc_final: 0.5381 (mmp) REVERT: A 499 LEU cc_start: 0.7275 (tt) cc_final: 0.6966 (tp) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.1204 time to fit residues: 12.3496 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 216 ASN ** 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 = 0.4697 r_free = 0.4697 target = 0.233380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.196564 restraints weight = 3733.736| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.96 r_work: 0.4257 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.223 Angle : 0.610 8.667 4654 Z= 0.290 Chirality : 0.041 0.173 544 Planarity : 0.004 0.031 574 Dihedral : 4.743 47.053 465 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.19 % Allowed : 22.03 % Favored : 74.78 % 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: 1.95 (0.43), residues: 425 helix: 1.60 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.76 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 50 HIS 0.006 0.001 HIS A 245 PHE 0.008 0.001 PHE A 362 TYR 0.009 0.001 TYR A 122 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.350 Fit side-chains REVERT: A 29 MET cc_start: 0.8280 (ttp) cc_final: 0.8057 (ttm) REVERT: A 56 ASN cc_start: 0.7344 (t0) cc_final: 0.6946 (t0) REVERT: A 169 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.6798 (mtt90) REVERT: A 222 MET cc_start: 0.5471 (ppp) cc_final: 0.4650 (mtm) REVERT: A 243 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: A 270 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.5228 (m-10) REVERT: A 474 MET cc_start: 0.6056 (mmp) cc_final: 0.5477 (mmp) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1220 time to fit residues: 12.4447 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.235526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.197753 restraints weight = 3722.470| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.98 r_work: 0.4263 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3408 Z= 0.179 Angle : 0.609 9.210 4654 Z= 0.283 Chirality : 0.042 0.194 544 Planarity : 0.004 0.030 574 Dihedral : 4.662 46.900 465 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 23.19 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.43), residues: 425 helix: 1.68 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.72 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.010 0.001 PHE A 362 TYR 0.007 0.001 TYR A 152 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.314 Fit side-chains REVERT: A 29 MET cc_start: 0.8296 (ttp) cc_final: 0.8053 (ttm) REVERT: A 56 ASN cc_start: 0.7317 (t0) cc_final: 0.6922 (t0) REVERT: A 169 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.6818 (mtt90) REVERT: A 222 MET cc_start: 0.5360 (ppp) cc_final: 0.4552 (mtm) REVERT: A 230 ARG cc_start: 0.6702 (tmt-80) cc_final: 0.6283 (tpt170) REVERT: A 234 MET cc_start: 0.6770 (tpp) cc_final: 0.6560 (tpt) REVERT: A 270 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.5392 (m-10) REVERT: A 474 MET cc_start: 0.5922 (mmp) cc_final: 0.5387 (mmp) REVERT: A 499 LEU cc_start: 0.7233 (tt) cc_final: 0.6875 (tp) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1275 time to fit residues: 13.0319 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.242619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.202488 restraints weight = 3636.322| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.18 r_work: 0.4243 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3408 Z= 0.169 Angle : 0.626 9.194 4654 Z= 0.283 Chirality : 0.041 0.186 544 Planarity : 0.004 0.030 574 Dihedral : 4.602 46.940 465 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.32 % Allowed : 24.06 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.43), residues: 425 helix: 1.76 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.66 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.010 0.001 PHE A 362 TYR 0.008 0.001 TYR A 152 ARG 0.001 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.358 Fit side-chains REVERT: A 29 MET cc_start: 0.8175 (ttp) cc_final: 0.7908 (ttm) REVERT: A 56 ASN cc_start: 0.7113 (t0) cc_final: 0.6703 (t0) REVERT: A 169 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.6879 (mtt90) REVERT: A 222 MET cc_start: 0.5180 (ppp) cc_final: 0.4376 (mtm) REVERT: A 270 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: A 394 MET cc_start: 0.6211 (tmm) cc_final: 0.5843 (tmm) REVERT: A 499 LEU cc_start: 0.7069 (tt) cc_final: 0.6746 (tp) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.1338 time to fit residues: 12.9709 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.240355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.199942 restraints weight = 3620.033| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 3.20 r_work: 0.4178 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3408 Z= 0.202 Angle : 0.633 8.182 4654 Z= 0.292 Chirality : 0.042 0.175 544 Planarity : 0.004 0.028 574 Dihedral : 4.630 46.953 465 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 24.06 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 425 helix: 1.72 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.62 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.008 0.001 PHE A 362 TYR 0.007 0.001 TYR A 152 ARG 0.002 0.000 ARG A 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.348 Fit side-chains REVERT: A 29 MET cc_start: 0.8187 (ttp) cc_final: 0.7917 (ttm) REVERT: A 56 ASN cc_start: 0.7066 (t0) cc_final: 0.6630 (t0) REVERT: A 169 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.6915 (mtt90) REVERT: A 222 MET cc_start: 0.5250 (ppp) cc_final: 0.4393 (mtm) REVERT: A 270 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: A 394 MET cc_start: 0.6088 (tmm) cc_final: 0.5728 (tmm) REVERT: A 499 LEU cc_start: 0.7110 (tt) cc_final: 0.6814 (tp) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.1284 time to fit residues: 12.5883 Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 11 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.238472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.198515 restraints weight = 3573.660| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.11 r_work: 0.4205 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3408 Z= 0.206 Angle : 0.661 10.641 4654 Z= 0.301 Chirality : 0.042 0.195 544 Planarity : 0.004 0.028 574 Dihedral : 4.663 47.267 465 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 24.64 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 425 helix: 1.73 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.57 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 495 HIS 0.003 0.001 HIS A 47 PHE 0.009 0.001 PHE A 362 TYR 0.006 0.001 TYR A 152 ARG 0.002 0.000 ARG A 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.24 seconds wall clock time: 33 minutes 12.07 seconds (1992.07 seconds total)