Starting phenix.real_space_refine on Wed Mar 5 18:27:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdv_61399/03_2025/9jdv_61399_trim.cif" } resolution = 3.32 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= 0.003 sd= 0.060 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2164 2.51 5 N 558 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 7 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: 3311 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.55, per 1000 atoms: 0.77 Number of scatterers: 3311 At special positions: 0 Unit cell: (94.17, 51.1, 66.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 561 8.00 N 558 7.00 C 2164 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 365.9 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 82.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 4.267A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 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 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 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.069A 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 Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.801A pdb=" N ALA A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) 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: 3.858A pdb=" N ARG A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.601A 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: 4.255A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 3.515A pdb=" N THR A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.070A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.221A 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: 3.548A pdb=" N ARG A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.573A 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: 3.723A pdb=" N ARG A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 684 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: 0.86 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 499 1.30 - 1.43: 900 1.43 - 1.55: 1954 1.55 - 1.68: 0 1.68 - 1.81: 44 Bond restraints: 3397 Sorted by residual: bond pdb=" CA SER A 242 " pdb=" C SER A 242 " ideal model delta sigma weight residual 1.523 1.438 0.086 1.34e-02 5.57e+03 4.08e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.465 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" N PHE A 241 " pdb=" CA PHE A 241 " ideal model delta sigma weight residual 1.457 1.387 0.070 1.29e-02 6.01e+03 2.97e+01 bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.456 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.478 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 4555 2.10 - 4.20: 55 4.20 - 6.30: 20 6.30 - 8.40: 6 8.40 - 10.50: 2 Bond angle restraints: 4638 Sorted by residual: angle pdb=" N ARG A 477 " pdb=" CA ARG A 477 " pdb=" C ARG A 477 " ideal model delta sigma weight residual 111.14 104.52 6.62 1.08e+00 8.57e-01 3.76e+01 angle pdb=" C ALA A 476 " pdb=" N ARG A 477 " pdb=" CA ARG A 477 " ideal model delta sigma weight residual 120.44 115.34 5.10 1.36e+00 5.41e-01 1.41e+01 angle pdb=" N PHE A 241 " pdb=" CA PHE A 241 " pdb=" C PHE A 241 " ideal model delta sigma weight residual 110.80 103.28 7.52 2.13e+00 2.20e-01 1.25e+01 angle pdb=" C2 URC A 601 " pdb=" N1 URC A 601 " pdb=" C6 URC A 601 " ideal model delta sigma weight residual 129.31 118.81 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C SER A 266 " pdb=" N VAL A 267 " pdb=" CA VAL A 267 " ideal model delta sigma weight residual 120.24 122.31 -2.07 6.30e-01 2.52e+00 1.08e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1775 17.81 - 35.63: 156 35.63 - 53.44: 32 53.44 - 71.25: 5 71.25 - 89.07: 3 Dihedral angle restraints: 1971 sinusoidal: 735 harmonic: 1236 Sorted by residual: 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 -140.99 54.99 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 127.97 -34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C SER A 242 " pdb=" N SER A 242 " pdb=" CA SER A 242 " pdb=" CB SER A 242 " ideal model delta harmonic sigma weight residual -122.60 -114.32 -8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 1968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 347 0.027 - 0.054: 129 0.054 - 0.081: 43 0.081 - 0.108: 23 0.108 - 0.135: 2 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 2.58 -0.13 2.00e-01 2.50e+01 4.53e-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 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 541 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 239 " 0.027 2.00e-02 2.50e+03 5.59e-02 3.13e+01 pdb=" C LEU A 239 " -0.097 2.00e-02 2.50e+03 pdb=" O LEU A 239 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY A 240 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 241 " -0.005 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 241 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 241 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 241 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 241 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 241 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 268 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.016 5.00e-02 4.00e+02 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3402 3.25 - 3.80: 5480 3.80 - 4.35: 6879 4.35 - 4.90: 11201 Nonbonded interactions: 27039 Sorted by model distance: nonbonded pdb=" O GLY A 240 " pdb=" C PHE A 241 " model vdw 2.150 3.270 nonbonded pdb=" CE2 PHE A 241 " pdb=" O13 URC A 601 " model vdw 2.168 2.672 nonbonded pdb=" O PHE A 241 " pdb=" C SER A 242 " model vdw 2.240 3.270 nonbonded pdb=" O SER A 242 " pdb=" N HIS A 245 " model vdw 2.262 3.120 nonbonded pdb=" O GLY A 240 " pdb=" N PHE A 243 " model vdw 2.272 3.120 ... (remaining 27034 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.006 0.113 3397 Z= 0.409 Angle : 0.706 10.503 4638 Z= 0.385 Chirality : 0.035 0.135 544 Planarity : 0.004 0.056 572 Dihedral : 13.991 89.067 1167 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.03 % Allowed : 9.28 % 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: -0.41 (0.40), residues: 425 helix: 0.02 (0.29), residues: 289 sheet: -2.23 (1.36), residues: 10 loop : -0.44 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 30 HIS 0.001 0.000 HIS A 428 PHE 0.023 0.001 PHE A 241 TYR 0.003 0.001 TYR A 152 ARG 0.001 0.000 ARG A 90 *********************** 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 110 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.319 Fit side-chains REVERT: A 29 MET cc_start: 0.7581 (ttp) cc_final: 0.7280 (ttp) REVERT: A 96 TRP cc_start: 0.4546 (m100) cc_final: 0.4252 (m-10) REVERT: A 343 MET cc_start: 0.2977 (tpt) cc_final: 0.1234 (tpp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.1531 time to fit residues: 19.7217 Evaluate side-chains 74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 424 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 39 ASN A 382 GLN A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.226216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192195 restraints weight = 4352.070| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.26 r_work: 0.4234 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3397 Z= 0.292 Angle : 0.695 7.486 4638 Z= 0.334 Chirality : 0.045 0.146 544 Planarity : 0.005 0.027 572 Dihedral : 5.434 55.606 464 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.64 % Allowed : 19.71 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.43), residues: 425 helix: 0.94 (0.31), residues: 297 sheet: -1.89 (1.53), residues: 10 loop : 0.63 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.007 0.001 HIS A 47 PHE 0.022 0.003 PHE A 40 TYR 0.022 0.002 TYR A 122 ARG 0.004 0.001 ARG A 84 *********************** 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 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4820 (m100) cc_final: 0.4197 (m-10) REVERT: A 181 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7257 (tt) REVERT: A 234 MET cc_start: 0.6536 (tpp) cc_final: 0.6253 (tpp) REVERT: A 343 MET cc_start: 0.2930 (tpt) cc_final: 0.1486 (tpp) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.0958 time to fit residues: 11.0698 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.227268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.193628 restraints weight = 4273.179| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 3.33 r_work: 0.4263 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3397 Z= 0.171 Angle : 0.606 7.612 4638 Z= 0.286 Chirality : 0.040 0.129 544 Planarity : 0.004 0.031 572 Dihedral : 5.229 53.541 463 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.19 % Allowed : 23.48 % Favored : 73.33 % 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: 1.56 (0.31), residues: 293 sheet: -2.21 (1.65), residues: 10 loop : 0.98 (0.66), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 495 HIS 0.002 0.001 HIS A 492 PHE 0.020 0.002 PHE A 358 TYR 0.006 0.001 TYR A 122 ARG 0.002 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 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4636 (m100) cc_final: 0.4071 (m-10) REVERT: A 149 GLN cc_start: 0.7881 (mt0) cc_final: 0.7633 (mp10) REVERT: A 181 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7132 (tt) REVERT: A 215 MET cc_start: 0.7592 (tpp) cc_final: 0.7390 (tpp) REVERT: A 343 MET cc_start: 0.2861 (tpt) cc_final: 0.1436 (tpp) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.1049 time to fit residues: 10.8490 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.224605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.189595 restraints weight = 4450.998| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 3.42 r_work: 0.4211 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3397 Z= 0.193 Angle : 0.597 7.262 4638 Z= 0.286 Chirality : 0.040 0.132 544 Planarity : 0.004 0.030 572 Dihedral : 4.701 40.056 463 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.77 % Allowed : 24.06 % Favored : 72.17 % 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: 1.68 (0.31), residues: 296 sheet: -2.10 (1.80), residues: 10 loop : 0.98 (0.67), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.017 0.002 PHE A 358 TYR 0.013 0.001 TYR A 152 ARG 0.005 0.000 ARG A 203 *********************** 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 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4545 (m100) cc_final: 0.3926 (m-10) REVERT: A 149 GLN cc_start: 0.7996 (mt0) cc_final: 0.7740 (mp10) REVERT: A 181 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 215 MET cc_start: 0.7705 (tpp) cc_final: 0.7449 (tpp) REVERT: A 343 MET cc_start: 0.2885 (tpt) cc_final: 0.1494 (tpp) REVERT: A 372 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8016 (tp-100) REVERT: A 421 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7940 (mp) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.1067 time to fit residues: 10.5207 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.224709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.190909 restraints weight = 4341.100| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.36 r_work: 0.4230 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3397 Z= 0.166 Angle : 0.566 7.674 4638 Z= 0.273 Chirality : 0.039 0.129 544 Planarity : 0.004 0.032 572 Dihedral : 4.435 44.749 462 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.48 % Allowed : 25.51 % Favored : 71.01 % 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: 2.19 (0.44), residues: 425 helix: 1.82 (0.31), residues: 296 sheet: -2.06 (1.83), residues: 10 loop : 1.07 (0.69), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.002 0.001 HIS A 492 PHE 0.013 0.002 PHE A 358 TYR 0.014 0.001 TYR A 152 ARG 0.001 0.000 ARG A 477 *********************** 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 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7727 (ttm) cc_final: 0.7391 (ttp) REVERT: A 96 TRP cc_start: 0.4520 (m100) cc_final: 0.3881 (m-10) REVERT: A 149 GLN cc_start: 0.7964 (mt0) cc_final: 0.7709 (mp10) REVERT: A 181 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7034 (tt) REVERT: A 215 MET cc_start: 0.7743 (tpp) cc_final: 0.7463 (tpp) REVERT: A 343 MET cc_start: 0.2879 (tpt) cc_final: 0.1500 (tpp) REVERT: A 372 GLN cc_start: 0.8381 (tp-100) cc_final: 0.7955 (tp-100) REVERT: A 421 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.0979 time to fit residues: 10.7820 Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.220204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185451 restraints weight = 4453.233| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 3.39 r_work: 0.4170 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3397 Z= 0.216 Angle : 0.605 7.664 4638 Z= 0.293 Chirality : 0.041 0.116 544 Planarity : 0.005 0.035 572 Dihedral : 4.476 47.069 461 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.80 % Allowed : 25.51 % Favored : 68.70 % 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: 2.05 (0.44), residues: 425 helix: 1.69 (0.31), residues: 296 sheet: -2.33 (1.70), residues: 10 loop : 1.12 (0.69), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.004 0.001 HIS A 245 PHE 0.016 0.002 PHE A 241 TYR 0.014 0.001 TYR A 122 ARG 0.003 0.000 ARG A 124 *********************** 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 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ILE cc_start: 0.5736 (OUTLIER) cc_final: 0.5423 (mm) REVERT: A 96 TRP cc_start: 0.4600 (m100) cc_final: 0.3935 (m-10) REVERT: A 149 GLN cc_start: 0.8030 (mt0) cc_final: 0.7766 (mp10) REVERT: A 181 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7104 (tt) REVERT: A 215 MET cc_start: 0.7823 (tpp) cc_final: 0.7428 (tpp) REVERT: A 343 MET cc_start: 0.2930 (tpt) cc_final: 0.1489 (tpp) REVERT: A 372 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8018 (tp-100) outliers start: 20 outliers final: 13 residues processed: 81 average time/residue: 0.1119 time to fit residues: 11.9297 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.219044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184897 restraints weight = 4391.175| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 3.38 r_work: 0.4172 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3397 Z= 0.203 Angle : 0.602 6.312 4638 Z= 0.293 Chirality : 0.041 0.131 544 Planarity : 0.004 0.035 572 Dihedral : 4.567 51.356 461 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.22 % Allowed : 26.09 % Favored : 68.70 % 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: 2.01 (0.44), residues: 425 helix: 1.66 (0.31), residues: 296 sheet: -2.36 (1.75), residues: 10 loop : 1.11 (0.69), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 50 HIS 0.003 0.001 HIS A 245 PHE 0.022 0.002 PHE A 449 TYR 0.018 0.002 TYR A 152 ARG 0.002 0.000 ARG A 172 *********************** 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 93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7801 (ttm) cc_final: 0.7542 (ttp) REVERT: A 77 ILE cc_start: 0.5767 (OUTLIER) cc_final: 0.5493 (mm) REVERT: A 96 TRP cc_start: 0.4544 (m100) cc_final: 0.3851 (m-10) REVERT: A 149 GLN cc_start: 0.8009 (mt0) cc_final: 0.7721 (mp10) REVERT: A 181 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7078 (tt) REVERT: A 215 MET cc_start: 0.7842 (tpp) cc_final: 0.7464 (tpp) REVERT: A 267 VAL cc_start: 0.8460 (t) cc_final: 0.8210 (m) REVERT: A 343 MET cc_start: 0.2979 (tpt) cc_final: 0.1567 (tpp) REVERT: A 372 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8058 (tp-100) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.1070 time to fit residues: 11.8486 Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.217254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.181671 restraints weight = 4418.812| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.37 r_work: 0.4133 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3397 Z= 0.234 Angle : 0.641 6.373 4638 Z= 0.311 Chirality : 0.043 0.157 544 Planarity : 0.004 0.035 572 Dihedral : 4.715 51.972 461 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.93 % Allowed : 27.83 % Favored : 67.25 % 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 (0.44), residues: 425 helix: 1.64 (0.31), residues: 293 sheet: -2.40 (1.76), residues: 10 loop : 1.23 (0.69), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.002 0.001 HIS A 245 PHE 0.017 0.002 PHE A 241 TYR 0.013 0.002 TYR A 122 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 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7836 (ttm) cc_final: 0.7578 (ttp) REVERT: A 77 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5679 (mm) REVERT: A 96 TRP cc_start: 0.4593 (m100) cc_final: 0.3848 (m-10) REVERT: A 149 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: A 181 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7140 (tt) REVERT: A 215 MET cc_start: 0.7916 (tpp) cc_final: 0.7550 (tpp) REVERT: A 343 MET cc_start: 0.2894 (tpt) cc_final: 0.1499 (tpp) REVERT: A 372 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8073 (tp-100) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.1117 time to fit residues: 12.5140 Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL 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 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.218238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.182685 restraints weight = 4392.243| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 3.37 r_work: 0.4146 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3397 Z= 0.212 Angle : 0.663 10.556 4638 Z= 0.315 Chirality : 0.043 0.187 544 Planarity : 0.004 0.034 572 Dihedral : 4.708 54.631 461 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.93 % Allowed : 28.99 % Favored : 66.09 % 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: 1.96 (0.44), residues: 425 helix: 1.60 (0.31), residues: 294 sheet: -2.45 (1.81), residues: 10 loop : 1.18 (0.68), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 50 HIS 0.003 0.001 HIS A 86 PHE 0.015 0.002 PHE A 241 TYR 0.014 0.001 TYR A 152 ARG 0.001 0.000 ARG A 89 *********************** 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 94 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7824 (ttm) cc_final: 0.7569 (ttp) REVERT: A 77 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5647 (mm) REVERT: A 96 TRP cc_start: 0.4560 (m100) cc_final: 0.3896 (m-10) REVERT: A 149 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: A 181 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7100 (tt) REVERT: A 215 MET cc_start: 0.7882 (tpp) cc_final: 0.7513 (tpp) REVERT: A 343 MET cc_start: 0.2832 (tpt) cc_final: 0.1676 (tpp) REVERT: A 372 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8057 (tp-100) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.1176 time to fit residues: 13.0905 Evaluate side-chains 92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.0070 chunk 11 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.221539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.187526 restraints weight = 4333.979| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.35 r_work: 0.4186 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3397 Z= 0.169 Angle : 0.653 9.725 4638 Z= 0.306 Chirality : 0.041 0.176 544 Planarity : 0.004 0.031 572 Dihedral : 4.604 57.027 461 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.90 % Allowed : 30.72 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.44), residues: 425 helix: 1.63 (0.31), residues: 301 sheet: -2.15 (1.89), residues: 10 loop : 1.10 (0.69), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 50 HIS 0.002 0.000 HIS A 86 PHE 0.017 0.002 PHE A 360 TYR 0.015 0.001 TYR A 152 ARG 0.007 0.000 ARG A 465 ********************** 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 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.5199 (tpp) cc_final: 0.4758 (tpp) REVERT: A 29 MET cc_start: 0.7751 (ttm) cc_final: 0.7516 (ttp) REVERT: A 96 TRP cc_start: 0.4624 (m100) cc_final: 0.3957 (m-10) REVERT: A 149 GLN cc_start: 0.7964 (mt0) cc_final: 0.7739 (mp10) REVERT: A 181 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7083 (tt) REVERT: A 215 MET cc_start: 0.7864 (tpp) cc_final: 0.7483 (tpp) REVERT: A 343 MET cc_start: 0.2789 (tpt) cc_final: 0.1631 (tpp) REVERT: A 372 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8024 (tp-100) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1151 time to fit residues: 12.1923 Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.217209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181897 restraints weight = 4435.597| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.35 r_work: 0.4129 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3397 Z= 0.236 Angle : 0.688 9.566 4638 Z= 0.325 Chirality : 0.043 0.177 544 Planarity : 0.004 0.035 572 Dihedral : 4.703 55.780 461 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.06 % Allowed : 30.14 % Favored : 65.80 % 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: 1.92 (0.44), residues: 425 helix: 1.55 (0.31), residues: 299 sheet: -2.39 (1.87), residues: 10 loop : 1.19 (0.69), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.002 0.001 HIS A 245 PHE 0.019 0.002 PHE A 241 TYR 0.014 0.001 TYR A 152 ARG 0.009 0.000 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.29 seconds wall clock time: 30 minutes 25.23 seconds (1825.23 seconds total)