Starting phenix.real_space_refine on Mon Jan 13 16:31:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9je0_61403/01_2025/9je0_61403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9je0_61403/01_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_61403/01_2025/9je0_61403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9je0_61403/01_2025/9je0_61403.map" model { file = "/net/cci-nas-00/data/ceres_data/9je0_61403/01_2025/9je0_61403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9je0_61403/01_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-5571/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: 2.84, per 1000 atoms: 0.86 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: 0.90 Conformation dependent library (CDL) restraints added in 409.0 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: 0.32 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: 0.91 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: 0.810 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.830 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- 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 : 0.320 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: 0.1494 time to fit residues: 18.7606 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 : 0.313 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.210658 restraints weight = 3611.725| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.90 r_work: 0.4367 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 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 : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7924 (ttp) cc_final: 0.7713 (ttm) REVERT: A 82 ASN cc_start: 0.6179 (m-40) cc_final: 0.5837 (p0) REVERT: A 118 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6837 (t0) REVERT: A 149 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: A 169 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6574 (mtt90) REVERT: A 222 MET cc_start: 0.5217 (ppp) cc_final: 0.4410 (mtm) REVERT: A 270 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.5132 (m-10) REVERT: A 342 ARG cc_start: 0.6467 (ptt90) cc_final: 0.4459 (ptt90) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 0.1244 time to fit residues: 13.0454 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 : 0.331 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.243492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.207530 restraints weight = 3665.818| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 2.91 r_work: 0.4348 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3408 Z= 0.170 Angle : 0.560 6.165 4654 Z= 0.267 Chirality : 0.038 0.121 544 Planarity : 0.004 0.030 574 Dihedral : 5.818 70.560 467 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.77 % Allowed : 18.84 % Favored : 77.39 % 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: 1.58 (0.42), residues: 425 helix: 1.45 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.27 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.002 0.000 HIS A 47 PHE 0.016 0.001 PHE A 362 TYR 0.011 0.001 TYR A 122 ARG 0.006 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 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7984 (ttp) cc_final: 0.7763 (ttm) REVERT: A 50 TRP cc_start: 0.7174 (t60) cc_final: 0.6583 (t60) REVERT: A 82 ASN cc_start: 0.6179 (m-40) cc_final: 0.5758 (p0) REVERT: A 149 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: A 169 ARG cc_start: 0.7271 (mmm-85) cc_final: 0.6483 (mtt90) REVERT: A 222 MET cc_start: 0.5249 (ppp) cc_final: 0.4525 (mtp) REVERT: A 270 PHE cc_start: 0.5564 (OUTLIER) cc_final: 0.5119 (m-10) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.1152 time to fit residues: 12.0308 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 156 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.4759 r_free = 0.4759 target = 0.243292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.206339 restraints weight = 3773.398| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.01 r_work: 0.4339 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3408 Z= 0.160 Angle : 0.561 6.690 4654 Z= 0.266 Chirality : 0.038 0.123 544 Planarity : 0.004 0.029 574 Dihedral : 5.272 51.682 467 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.90 % Allowed : 20.87 % Favored : 76.23 % 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: 1.77 (0.42), residues: 425 helix: 1.58 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.35 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 495 HIS 0.001 0.000 HIS A 245 PHE 0.014 0.001 PHE A 362 TYR 0.009 0.001 TYR A 122 ARG 0.001 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 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.7976 (ttp) cc_final: 0.7761 (ttm) REVERT: A 82 ASN cc_start: 0.6196 (m-40) cc_final: 0.5553 (t0) REVERT: A 149 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6864 (mt0) REVERT: A 169 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.6590 (mtt90) REVERT: A 186 MET cc_start: 0.7963 (mmm) cc_final: 0.7626 (mmp) REVERT: A 222 MET cc_start: 0.5254 (ppp) cc_final: 0.4466 (mtm) REVERT: A 270 PHE cc_start: 0.5531 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: A 342 ARG cc_start: 0.6485 (ptt90) cc_final: 0.4510 (ptt90) REVERT: A 394 MET cc_start: 0.6350 (tmm) cc_final: 0.5588 (tmm) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.1335 time to fit residues: 13.2843 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 : 0.349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4731 r_free = 0.4731 target = 0.239351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.202629 restraints weight = 3773.890| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 3.01 r_work: 0.4298 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3001 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= 0.182 Angle : 0.569 6.804 4654 Z= 0.272 Chirality : 0.039 0.119 544 Planarity : 0.004 0.031 574 Dihedral : 4.812 43.127 465 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.90 % Allowed : 22.61 % Favored : 74.49 % 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: 1.90 (0.43), residues: 425 helix: 1.62 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.57 (0.64), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 362 TYR 0.010 0.001 TYR A 122 ARG 0.001 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 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.354 Fit side-chains REVERT: A 29 MET cc_start: 0.8014 (ttp) cc_final: 0.7805 (ttm) REVERT: A 38 GLU cc_start: 0.7641 (tp30) cc_final: 0.7336 (tp30) REVERT: A 82 ASN cc_start: 0.6227 (m-40) cc_final: 0.5530 (t0) REVERT: A 149 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6945 (mt0) REVERT: A 169 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.6679 (mtt90) REVERT: A 186 MET cc_start: 0.7963 (mmm) cc_final: 0.7692 (mmp) REVERT: A 222 MET cc_start: 0.5388 (ppp) cc_final: 0.4567 (mtm) REVERT: A 270 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: A 394 MET cc_start: 0.6382 (tmm) cc_final: 0.5593 (tmm) REVERT: A 474 MET cc_start: 0.5852 (mmp) cc_final: 0.5380 (mmp) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.1216 time to fit residues: 12.4208 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 LEU 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: 2.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.4739 r_free = 0.4739 target = 0.238259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.202207 restraints weight = 3859.181| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 3.02 r_work: 0.4295 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3197 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= 0.174 Angle : 0.578 7.351 4654 Z= 0.274 Chirality : 0.039 0.121 544 Planarity : 0.004 0.032 574 Dihedral : 4.667 43.315 465 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 22.61 % Favored : 74.49 % 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: 1.65 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.61 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.002 0.001 HIS A 47 PHE 0.010 0.001 PHE A 362 TYR 0.008 0.001 TYR A 122 ARG 0.001 0.000 ARG A 434 *********************** 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 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.328 Fit side-chains REVERT: A 29 MET cc_start: 0.8148 (ttp) cc_final: 0.7916 (ttm) REVERT: A 36 MET cc_start: 0.7456 (mmt) cc_final: 0.6848 (tpp) REVERT: A 38 GLU cc_start: 0.7610 (tp30) cc_final: 0.7333 (tp30) REVERT: A 56 ASN cc_start: 0.7356 (t0) cc_final: 0.6953 (t0) REVERT: A 149 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: A 169 ARG cc_start: 0.7470 (mmm-85) cc_final: 0.6713 (mtt90) REVERT: A 186 MET cc_start: 0.7942 (mmm) cc_final: 0.7699 (mmp) REVERT: A 222 MET cc_start: 0.5400 (ppp) cc_final: 0.4607 (mtm) REVERT: A 270 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.5056 (m-80) REVERT: A 394 MET cc_start: 0.6417 (tmm) cc_final: 0.5613 (tmm) REVERT: A 499 LEU cc_start: 0.7296 (tt) cc_final: 0.6945 (tp) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1216 time to fit residues: 12.2554 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP 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 442 LEU 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: 0.0670 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 = 0.4728 r_free = 0.4728 target = 0.237288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.201454 restraints weight = 3759.852| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.99 r_work: 0.4285 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3357 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= 0.180 Angle : 0.589 8.432 4654 Z= 0.278 Chirality : 0.039 0.121 544 Planarity : 0.004 0.031 574 Dihedral : 4.683 46.491 465 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 21.74 % Favored : 75.07 % 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: 2.00 (0.43), residues: 425 helix: 1.69 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.65 (0.65), 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 122 ARG 0.002 0.000 ARG A 477 *********************** 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 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.366 Fit side-chains REVERT: A 29 MET cc_start: 0.8240 (ttp) cc_final: 0.8005 (ttm) REVERT: A 38 GLU cc_start: 0.7588 (tp30) cc_final: 0.7304 (tp30) REVERT: A 56 ASN cc_start: 0.7324 (t0) cc_final: 0.6924 (t0) REVERT: A 149 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7057 (mt0) REVERT: A 169 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.6772 (mtt90) REVERT: A 222 MET cc_start: 0.5404 (ppp) cc_final: 0.4604 (mtm) REVERT: A 270 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: A 499 LEU cc_start: 0.7280 (tt) cc_final: 0.6950 (tp) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.1220 time to fit residues: 12.8815 Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 248 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4677 r_free = 0.4677 target = 0.233242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.196279 restraints weight = 3712.380| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.93 r_work: 0.4253 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3408 Z= 0.230 Angle : 0.648 7.552 4654 Z= 0.304 Chirality : 0.041 0.163 544 Planarity : 0.004 0.030 574 Dihedral : 4.746 46.745 465 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.61 % Allowed : 22.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.43), residues: 425 helix: 1.61 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.71 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.008 0.001 PHE A 362 TYR 0.010 0.001 TYR A 122 ARG 0.002 0.000 ARG A 477 *********************** 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 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.352 Fit side-chains REVERT: A 29 MET cc_start: 0.8222 (ttp) cc_final: 0.8006 (ttm) REVERT: A 38 GLU cc_start: 0.7608 (tp30) cc_final: 0.7364 (tp30) REVERT: A 56 ASN cc_start: 0.7370 (t0) cc_final: 0.6956 (t0) REVERT: A 149 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: A 169 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.6808 (mtt90) REVERT: A 222 MET cc_start: 0.5447 (ppp) cc_final: 0.4623 (mtm) REVERT: A 230 ARG cc_start: 0.6749 (tmt-80) cc_final: 0.6193 (tpt170) REVERT: A 270 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.5258 (m-10) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.1290 time to fit residues: 13.2777 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 : 0.374 ------------------------------------------------------------------------------- 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 248 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4652 r_free = 0.4652 target = 0.239822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.200341 restraints weight = 3674.286| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 3.07 r_work: 0.4210 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3408 Z= 0.204 Angle : 0.644 9.528 4654 Z= 0.300 Chirality : 0.041 0.190 544 Planarity : 0.004 0.030 574 Dihedral : 4.714 46.433 465 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.19 % Allowed : 24.06 % Favored : 72.75 % 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: 1.95 (0.43), residues: 425 helix: 1.63 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.68 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 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 0.003 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 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.341 Fit side-chains REVERT: A 29 MET cc_start: 0.8152 (ttp) cc_final: 0.7865 (ttm) REVERT: A 38 GLU cc_start: 0.7719 (tp30) cc_final: 0.7299 (tp30) REVERT: A 56 ASN cc_start: 0.7058 (t0) cc_final: 0.6631 (t0) REVERT: A 118 ASP cc_start: 0.7721 (t0) cc_final: 0.7445 (t0) REVERT: A 149 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: A 169 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.6887 (mtt90) REVERT: A 222 MET cc_start: 0.5179 (ppp) cc_final: 0.4374 (mtm) REVERT: A 234 MET cc_start: 0.6428 (tpp) cc_final: 0.6227 (tpt) REVERT: A 270 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: A 474 MET cc_start: 0.5293 (mmp) cc_final: 0.5052 (mmp) REVERT: A 499 LEU cc_start: 0.6993 (tt) cc_final: 0.6727 (tp) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.1245 time to fit residues: 12.7271 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 238 SER Chi-restraints excluded: chain A residue 248 THR 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 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: 3.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.240176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.200529 restraints weight = 3594.120| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 3.06 r_work: 0.4203 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3408 Z= 0.199 Angle : 0.655 9.074 4654 Z= 0.303 Chirality : 0.042 0.189 544 Planarity : 0.004 0.029 574 Dihedral : 4.692 46.575 465 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.32 % Allowed : 23.48 % 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: 1.93 (0.43), residues: 425 helix: 1.64 (0.30), residues: 298 sheet: None (None), residues: 0 loop : 0.62 (0.65), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.010 0.001 PHE A 362 TYR 0.006 0.001 TYR A 122 ARG 0.002 0.000 ARG A 477 ********************** 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 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.336 Fit side-chains REVERT: A 29 MET cc_start: 0.8154 (ttp) cc_final: 0.7860 (ttm) REVERT: A 38 GLU cc_start: 0.7724 (tp30) cc_final: 0.7314 (tp30) REVERT: A 56 ASN cc_start: 0.7079 (t0) cc_final: 0.6642 (t0) REVERT: A 118 ASP cc_start: 0.7715 (t0) cc_final: 0.7440 (t0) REVERT: A 169 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.6970 (mtt90) REVERT: A 222 MET cc_start: 0.5113 (ppp) cc_final: 0.4320 (mtm) REVERT: A 270 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: A 394 MET cc_start: 0.6109 (tmm) cc_final: 0.5752 (tmm) REVERT: A 474 MET cc_start: 0.5266 (mmp) cc_final: 0.5030 (mmp) REVERT: A 499 LEU cc_start: 0.7068 (tt) cc_final: 0.6800 (tp) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.1348 time to fit residues: 12.9546 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 : 0.344 ------------------------------------------------------------------------------- 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 442 LEU 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: 0.0370 chunk 15 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 26 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.1776 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.243629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.205294 restraints weight = 3487.608| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.96 r_work: 0.4235 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3908 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= 0.163 Angle : 0.643 9.787 4654 Z= 0.293 Chirality : 0.041 0.200 544 Planarity : 0.004 0.030 574 Dihedral : 4.596 47.007 465 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 2.08 (0.43), residues: 425 helix: 1.80 (0.31), residues: 299 sheet: None (None), residues: 0 loop : 0.54 (0.64), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 50 HIS 0.002 0.000 HIS A 245 PHE 0.009 0.001 PHE A 362 TYR 0.008 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: 1804.80 seconds wall clock time: 33 minutes 17.15 seconds (1997.15 seconds total)