Starting phenix.real_space_refine on Tue Feb 11 03:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.map" model { file = "/net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zha_14728/02_2025/7zha_14728.cif" } resolution = 3.55 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= 0.000 sd= 0.001 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 22 5.16 5 C 2543 2.51 5 N 632 2.21 5 O 639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3836 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3811 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain breaks: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'JDW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.90 Number of scatterers: 3836 At special positions: 0 Unit cell: (98.34, 64.02, 81.84, 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 22 16.00 O 639 8.00 N 632 7.00 C 2543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " 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: 1.08 Conformation dependent library (CDL) restraints added in 469.7 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 80.9% alpha, 0.8% 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 3 through 11 Processing helix chain 'A' and resid 15 through 42 removed outlier: 4.722A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 179 removed outlier: 4.039A pdb=" N ASP A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.976A pdb=" N PHE A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Proline residue: A 258 - end of helix removed outlier: 3.856A pdb=" N ILE A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 Proline residue: A 277 - end of helix removed outlier: 3.932A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 344 through 373 removed outlier: 3.942A pdb=" N MET A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 404 removed outlier: 3.842A pdb=" N LEU A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 406 through 427 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.339A pdb=" N THR A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 461 removed outlier: 3.763A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 495 Proline residue: A 485 - end of helix removed outlier: 3.914A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.831A pdb=" N ILE A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 527 through 535 removed outlier: 4.406A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 532 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 534 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 270 hydrogen bonds defined for protein. 792 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: 0.99 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1174 1.34 - 1.46: 782 1.46 - 1.58: 1947 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 3933 Sorted by residual: bond pdb=" C11 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.337 1.435 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C13 JDW A 601 " pdb=" N2 JDW A 601 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C3 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.382 1.451 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N ASP A 5 " pdb=" CA ASP A 5 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.76e+00 bond pdb=" C7 JDW A 601 " pdb=" C8 JDW A 601 " ideal model delta sigma weight residual 1.411 1.359 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 3928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 5103 1.50 - 3.01: 194 3.01 - 4.51: 39 4.51 - 6.02: 9 6.02 - 7.52: 8 Bond angle restraints: 5353 Sorted by residual: angle pdb=" CA MET A 248 " pdb=" CB MET A 248 " pdb=" CG MET A 248 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA ASP A 5 " pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 121.07 118.19 2.88 1.10e+00 8.26e-01 6.84e+00 angle pdb=" C TRP A 152 " pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta sigma weight residual 121.18 116.03 5.15 1.98e+00 2.55e-01 6.77e+00 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 111.91 109.63 2.28 8.90e-01 1.26e+00 6.57e+00 angle pdb=" CA THR A 528 " pdb=" CB THR A 528 " pdb=" CG2 THR A 528 " ideal model delta sigma weight residual 110.50 114.77 -4.27 1.70e+00 3.46e-01 6.31e+00 ... (remaining 5348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1997 15.84 - 31.69: 203 31.69 - 47.53: 57 47.53 - 63.37: 9 63.37 - 79.22: 5 Dihedral angle restraints: 2271 sinusoidal: 892 harmonic: 1379 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 127 " pdb=" CB CYS A 127 " ideal model delta sinusoidal sigma weight residual 93.00 43.38 49.62 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -125.09 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA ASN A 467 " pdb=" C ASN A 467 " pdb=" N PHE A 468 " pdb=" CA PHE A 468 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 534 0.060 - 0.119: 75 0.119 - 0.179: 9 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 619 Sorted by residual: chirality pdb=" CG LEU A 124 " pdb=" CB LEU A 124 " pdb=" CD1 LEU A 124 " pdb=" CD2 LEU A 124 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA MET A 153 " pdb=" N MET A 153 " pdb=" C MET A 153 " pdb=" CB MET A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB THR A 528 " pdb=" CA THR A 528 " pdb=" OG1 THR A 528 " pdb=" CG2 THR A 528 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 616 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 292 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.008 2.00e-02 2.50e+03 1.37e-02 3.77e+00 pdb=" CG TYR A 284 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 34 " -0.010 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE A 34 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 34 " -0.000 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1337 2.86 - 3.37: 4259 3.37 - 3.88: 6345 3.88 - 4.39: 6927 4.39 - 4.90: 11467 Nonbonded interactions: 30335 Sorted by model distance: nonbonded pdb=" O ARG A 343 " pdb=" OG1 THR A 344 " model vdw 2.352 3.040 nonbonded pdb=" NH1 ARG A 407 " pdb=" O LEU A 517 " model vdw 2.362 3.120 nonbonded pdb=" O LEU A 154 " pdb=" OG1 THR A 157 " model vdw 2.370 3.040 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.380 3.040 nonbonded pdb=" NE2 GLN A 18 " pdb=" O ILE A 233 " model vdw 2.395 3.120 ... (remaining 30330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.005 0.098 3933 Z= 0.309 Angle : 0.734 7.522 5353 Z= 0.377 Chirality : 0.044 0.299 619 Planarity : 0.005 0.076 660 Dihedral : 14.090 79.215 1383 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.50 % Allowed : 0.99 % Favored : 98.51 % 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: 1.39 (0.39), residues: 479 helix: 1.52 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.62 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.028 0.002 PHE A 34 TYR 0.031 0.002 TYR A 284 ARG 0.005 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 3 SER cc_start: 0.5832 (OUTLIER) cc_final: 0.4118 (p) REVERT: A 281 PHE cc_start: 0.8611 (m-10) cc_final: 0.8374 (m-80) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1278 time to fit residues: 16.0756 Evaluate side-chains 75 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 335 ASN ** A 414 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 = 0.4266 r_free = 0.4266 target = 0.178027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.156834 restraints weight = 6254.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161482 restraints weight = 2923.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164473 restraints weight = 1695.796| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3933 Z= 0.226 Angle : 0.673 8.094 5353 Z= 0.343 Chirality : 0.042 0.190 619 Planarity : 0.005 0.049 660 Dihedral : 4.495 24.444 537 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.47 % Allowed : 13.90 % Favored : 82.63 % 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: 1.68 (0.39), residues: 479 helix: 1.67 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.48 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.024 0.002 PHE A 34 TYR 0.016 0.002 TYR A 284 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.477 Fit side-chains REVERT: A 185 TYR cc_start: 0.7663 (t80) cc_final: 0.7423 (t80) REVERT: A 331 GLU cc_start: 0.8010 (tp30) cc_final: 0.7665 (tp30) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.1230 time to fit residues: 13.3109 Evaluate side-chains 71 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4283 r_free = 0.4283 target = 0.180187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159264 restraints weight = 6223.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163910 restraints weight = 2896.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.166852 restraints weight = 1669.569| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3933 Z= 0.190 Angle : 0.643 9.960 5353 Z= 0.321 Chirality : 0.040 0.151 619 Planarity : 0.004 0.040 660 Dihedral : 4.304 21.895 536 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.18 % Favored : 95.62 % Rotamer: Outliers : 3.97 % Allowed : 15.38 % Favored : 80.65 % 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: 1.83 (0.40), residues: 479 helix: 1.80 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.48 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 71 HIS 0.003 0.002 HIS A 48 PHE 0.024 0.002 PHE A 356 TYR 0.016 0.001 TYR A 284 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.7689 (t80) cc_final: 0.7369 (t80) REVERT: A 223 TRP cc_start: 0.8013 (t-100) cc_final: 0.7781 (t-100) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.1150 time to fit residues: 13.1031 Evaluate side-chains 78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4210 r_free = 0.4210 target = 0.173841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152941 restraints weight = 6309.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157428 restraints weight = 2949.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.160332 restraints weight = 1706.197| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3933 Z= 0.208 Angle : 0.650 10.992 5353 Z= 0.326 Chirality : 0.040 0.149 619 Planarity : 0.004 0.034 660 Dihedral : 4.247 20.741 536 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 4.71 % Allowed : 17.87 % Favored : 77.42 % 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: 1.79 (0.40), residues: 479 helix: 1.80 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.62 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 71 HIS 0.005 0.002 HIS A 48 PHE 0.019 0.002 PHE A 34 TYR 0.011 0.002 TYR A 284 ARG 0.005 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5499 (OUTLIER) cc_final: 0.5049 (m-10) REVERT: A 185 TYR cc_start: 0.7594 (t80) cc_final: 0.7302 (t80) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.1216 time to fit residues: 12.6487 Evaluate side-chains 78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 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 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4194 r_free = 0.4194 target = 0.172268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151161 restraints weight = 6446.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155776 restraints weight = 2992.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158704 restraints weight = 1722.809| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3933 Z= 0.222 Angle : 0.663 12.544 5353 Z= 0.331 Chirality : 0.040 0.150 619 Planarity : 0.004 0.036 660 Dihedral : 4.247 20.349 536 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 4.71 % Allowed : 19.60 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.40), residues: 479 helix: 1.71 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.71 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 152 HIS 0.006 0.003 HIS A 48 PHE 0.018 0.002 PHE A 41 TYR 0.019 0.002 TYR A 284 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5552 (OUTLIER) cc_final: 0.5083 (m-10) REVERT: A 131 TRP cc_start: 0.8031 (m100) cc_final: 0.7719 (m100) REVERT: A 185 TYR cc_start: 0.7608 (t80) cc_final: 0.7262 (t80) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1187 time to fit residues: 12.6024 Evaluate side-chains 81 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.0030 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4196 r_free = 0.4196 target = 0.172159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.151455 restraints weight = 6348.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155969 restraints weight = 2933.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158954 restraints weight = 1685.628| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3933 Z= 0.219 Angle : 0.665 12.281 5353 Z= 0.334 Chirality : 0.040 0.143 619 Planarity : 0.004 0.037 660 Dihedral : 4.272 19.959 536 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 4.47 % Allowed : 21.09 % Favored : 74.44 % 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: 1.65 (0.40), residues: 479 helix: 1.75 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.85 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.023 0.002 PHE A 356 TYR 0.018 0.002 TYR A 284 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5561 (OUTLIER) cc_final: 0.5100 (m-10) REVERT: A 131 TRP cc_start: 0.8022 (m100) cc_final: 0.7743 (m100) outliers start: 18 outliers final: 17 residues processed: 84 average time/residue: 0.1496 time to fit residues: 15.9282 Evaluate side-chains 86 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4193 r_free = 0.4193 target = 0.171829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151098 restraints weight = 6355.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155550 restraints weight = 2958.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158393 restraints weight = 1710.783| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3933 Z= 0.210 Angle : 0.671 13.549 5353 Z= 0.333 Chirality : 0.040 0.141 619 Planarity : 0.004 0.037 660 Dihedral : 4.246 19.345 536 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 5.71 % Allowed : 21.84 % Favored : 72.46 % 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: 1.74 (0.40), residues: 479 helix: 1.88 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -0.91 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.004 0.002 HIS A 48 PHE 0.020 0.002 PHE A 34 TYR 0.019 0.002 TYR A 284 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5554 (OUTLIER) cc_final: 0.5081 (m-10) outliers start: 23 outliers final: 15 residues processed: 85 average time/residue: 0.1503 time to fit residues: 16.1736 Evaluate side-chains 84 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4195 r_free = 0.4195 target = 0.172428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151535 restraints weight = 6356.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156063 restraints weight = 2977.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.159024 restraints weight = 1725.017| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3933 Z= 0.225 Angle : 0.688 12.672 5353 Z= 0.347 Chirality : 0.041 0.179 619 Planarity : 0.005 0.037 660 Dihedral : 4.322 19.102 536 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 4.22 % Allowed : 22.83 % Favored : 72.95 % 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: 1.60 (0.40), residues: 479 helix: 1.82 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.08 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.028 0.002 PHE A 34 TYR 0.044 0.002 TYR A 284 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5545 (OUTLIER) cc_final: 0.5079 (m-10) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.1486 time to fit residues: 14.7558 Evaluate side-chains 82 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4173 r_free = 0.4173 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.149420 restraints weight = 6368.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.153955 restraints weight = 3001.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156910 restraints weight = 1737.292| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3933 Z= 0.240 Angle : 0.707 14.925 5353 Z= 0.354 Chirality : 0.041 0.165 619 Planarity : 0.004 0.038 660 Dihedral : 4.339 19.176 536 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.01 % Favored : 94.78 % Rotamer: Outliers : 4.22 % Allowed : 22.08 % Favored : 73.70 % 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: 1.62 (0.40), residues: 479 helix: 1.81 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.00 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.027 0.002 PHE A 34 TYR 0.040 0.002 TYR A 284 ARG 0.002 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5593 (OUTLIER) cc_final: 0.5122 (m-10) outliers start: 17 outliers final: 15 residues processed: 78 average time/residue: 0.1434 time to fit residues: 14.3110 Evaluate side-chains 81 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 436 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 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 = 0.4195 r_free = 0.4195 target = 0.172354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151670 restraints weight = 6378.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156205 restraints weight = 2996.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159053 restraints weight = 1734.933| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3933 Z= 0.213 Angle : 0.697 15.026 5353 Z= 0.347 Chirality : 0.041 0.167 619 Planarity : 0.004 0.038 660 Dihedral : 4.333 18.135 536 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.80 % Favored : 94.78 % Rotamer: Outliers : 3.72 % Allowed : 23.08 % Favored : 73.20 % 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: 1.64 (0.40), residues: 479 helix: 1.84 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -0.91 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 71 HIS 0.004 0.002 HIS A 48 PHE 0.023 0.002 PHE A 34 TYR 0.034 0.002 TYR A 284 ARG 0.004 0.000 ARG A 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5519 (OUTLIER) cc_final: 0.5083 (m-10) REVERT: A 131 TRP cc_start: 0.7960 (m100) cc_final: 0.7695 (m100) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.1394 time to fit residues: 13.9691 Evaluate side-chains 84 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 414 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 = 0.4231 r_free = 0.4231 target = 0.175751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155245 restraints weight = 6251.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.159819 restraints weight = 2954.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162826 restraints weight = 1699.202| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3933 Z= 0.192 Angle : 0.678 15.370 5353 Z= 0.336 Chirality : 0.040 0.158 619 Planarity : 0.004 0.038 660 Dihedral : 4.222 16.466 536 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer: Outliers : 4.22 % Allowed : 22.83 % Favored : 72.95 % 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 (0.40), residues: 479 helix: 1.82 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.08 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 71 HIS 0.003 0.001 HIS A 48 PHE 0.027 0.001 PHE A 34 TYR 0.031 0.002 TYR A 284 ARG 0.003 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.19 seconds wall clock time: 28 minutes 58.85 seconds (1738.85 seconds total)