Starting phenix.real_space_refine on Wed Mar 5 22:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zha_14728/03_2025/7zha_14728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zha_14728/03_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_14728/03_2025/7zha_14728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2025/7zha_14728.map" model { file = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2025/7zha_14728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_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-5624/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: 3.47, 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: 1.15 Conformation dependent library (CDL) restraints added in 442.6 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: 0.37 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: 1.08 Time building geometry restraints manager: 1.32 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: 2.820 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.590 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- 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 : 0.401 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: 0.1234 time to fit residues: 15.2746 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 : 0.351 ------------------------------------------------------------------------------- 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 = 6254.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161520 restraints weight = 2923.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164468 restraints weight = 1690.656| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.434 Fit side-chains REVERT: A 185 TYR cc_start: 0.7663 (t80) cc_final: 0.7423 (t80) REVERT: A 331 GLU cc_start: 0.8009 (tp30) cc_final: 0.7666 (tp30) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.1253 time to fit residues: 13.5614 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.180184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159241 restraints weight = 6203.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163867 restraints weight = 2883.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166860 restraints weight = 1660.922| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1821 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= 0.193 Angle : 0.644 9.692 5353 Z= 0.322 Chirality : 0.040 0.157 619 Planarity : 0.004 0.040 660 Dihedral : 4.319 22.058 536 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.38 % Favored : 95.41 % Rotamer: Outliers : 3.97 % Allowed : 16.13 % Favored : 79.90 % 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: 1.85 (0.40), residues: 479 helix: 1.80 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.45 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 71 HIS 0.003 0.002 HIS A 48 PHE 0.024 0.002 PHE A 34 TYR 0.015 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 92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.7667 (t80) cc_final: 0.7431 (t80) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.1268 time to fit residues: 13.7642 Evaluate side-chains 80 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 HIS 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: 0.9980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4200 r_free = 0.4200 target = 0.172953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152044 restraints weight = 6362.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.156511 restraints weight = 2975.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159313 restraints weight = 1732.086| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2140 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= 0.221 Angle : 0.664 11.743 5353 Z= 0.332 Chirality : 0.041 0.156 619 Planarity : 0.004 0.035 660 Dihedral : 4.292 21.279 536 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 5.21 % Allowed : 17.12 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.40), residues: 479 helix: 1.80 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.66 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 71 HIS 0.009 0.004 HIS A 48 PHE 0.019 0.002 PHE A 34 TYR 0.018 0.002 TYR A 49 ARG 0.003 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: 21 poor density : 67 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5589 (OUTLIER) cc_final: 0.5113 (m-10) REVERT: A 185 TYR cc_start: 0.7701 (t80) cc_final: 0.7400 (t80) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.1174 time to fit residues: 11.8838 Evaluate side-chains 79 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 48 HIS 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 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 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: 0.6980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4199 r_free = 0.4199 target = 0.173098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152305 restraints weight = 6487.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.156853 restraints weight = 2979.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.159800 restraints weight = 1708.555| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3933 Z= 0.209 Angle : 0.659 13.201 5353 Z= 0.328 Chirality : 0.040 0.150 619 Planarity : 0.004 0.035 660 Dihedral : 4.236 20.506 536 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.59 % Favored : 95.20 % Rotamer: Outliers : 4.71 % Allowed : 18.36 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.40), residues: 479 helix: 1.73 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.73 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 71 HIS 0.003 0.002 HIS A 137 PHE 0.017 0.002 PHE A 34 TYR 0.019 0.002 TYR A 284 ARG 0.006 0.000 ARG A 87 *********************** 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 90 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5549 (OUTLIER) cc_final: 0.5083 (m-10) REVERT: A 131 TRP cc_start: 0.8011 (m100) cc_final: 0.7701 (m100) REVERT: A 185 TYR cc_start: 0.7680 (t80) cc_final: 0.7363 (t80) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1171 time to fit residues: 12.5887 Evaluate side-chains 83 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 246 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 276 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.0010 chunk 4 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.175549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154582 restraints weight = 6340.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159173 restraints weight = 2957.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.162206 restraints weight = 1704.687| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2469 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= 0.186 Angle : 0.651 12.712 5353 Z= 0.322 Chirality : 0.039 0.140 619 Planarity : 0.004 0.036 660 Dihedral : 4.178 18.895 536 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.59 % Favored : 95.20 % Rotamer: Outliers : 3.97 % Allowed : 21.09 % Favored : 74.94 % 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: 1.76 (0.40), residues: 479 helix: 1.83 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -0.81 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 71 HIS 0.002 0.001 HIS A 48 PHE 0.020 0.002 PHE A 34 TYR 0.017 0.002 TYR A 284 ARG 0.002 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 92 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5424 (OUTLIER) cc_final: 0.5014 (m-10) REVERT: A 131 TRP cc_start: 0.7923 (m100) cc_final: 0.7653 (m100) REVERT: A 185 TYR cc_start: 0.7718 (t80) cc_final: 0.7351 (t80) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.1390 time to fit residues: 14.8514 Evaluate side-chains 84 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 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 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 = 0.4186 r_free = 0.4186 target = 0.171368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150397 restraints weight = 6378.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154895 restraints weight = 2979.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157825 restraints weight = 1729.290| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3933 Z= 0.227 Angle : 0.686 13.091 5353 Z= 0.343 Chirality : 0.041 0.141 619 Planarity : 0.004 0.036 660 Dihedral : 4.281 19.407 536 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.59 % Favored : 95.20 % Rotamer: Outliers : 4.71 % Allowed : 21.59 % 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: 1.72 (0.40), residues: 479 helix: 1.87 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -0.89 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 71 HIS 0.002 0.001 HIS A 137 PHE 0.025 0.002 PHE A 356 TYR 0.045 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 88 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5581 (OUTLIER) cc_final: 0.5144 (m-10) REVERT: A 131 TRP cc_start: 0.8048 (m100) cc_final: 0.7790 (m100) REVERT: A 185 TYR cc_start: 0.7573 (t80) cc_final: 0.7309 (t80) outliers start: 19 outliers final: 15 residues processed: 81 average time/residue: 0.1438 time to fit residues: 14.7422 Evaluate side-chains 82 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 363 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 438 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 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 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 = 0.4192 r_free = 0.4192 target = 0.172320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151606 restraints weight = 6340.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.156122 restraints weight = 2938.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158915 restraints weight = 1691.657| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3933 Z= 0.224 Angle : 0.694 14.110 5353 Z= 0.346 Chirality : 0.041 0.151 619 Planarity : 0.004 0.037 660 Dihedral : 4.297 19.245 536 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.37 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: 1.68 (0.40), residues: 479 helix: 1.88 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.04 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 71 HIS 0.003 0.002 HIS A 48 PHE 0.023 0.002 PHE A 356 TYR 0.036 0.002 TYR A 284 ARG 0.003 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 86 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.5111 (m-10) REVERT: A 131 TRP cc_start: 0.8045 (m100) cc_final: 0.7784 (m100) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1263 time to fit residues: 12.9001 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 : 0.395 ------------------------------------------------------------------------------- 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 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 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4203 r_free = 0.4203 target = 0.173562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.152967 restraints weight = 6337.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157419 restraints weight = 2934.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.160252 restraints weight = 1684.489| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3933 Z= 0.213 Angle : 0.693 14.060 5353 Z= 0.345 Chirality : 0.041 0.187 619 Planarity : 0.004 0.037 660 Dihedral : 4.325 18.620 536 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.18 % Favored : 95.41 % Rotamer: Outliers : 3.72 % Allowed : 20.84 % Favored : 75.43 % 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: 1.63 (0.40), residues: 479 helix: 1.87 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.16 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 71 HIS 0.002 0.001 HIS A 48 PHE 0.022 0.002 PHE A 356 TYR 0.035 0.002 TYR A 284 ARG 0.003 0.000 ARG A 128 *********************** 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 83 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5500 (OUTLIER) cc_final: 0.5092 (m-10) REVERT: A 131 TRP cc_start: 0.8007 (m100) cc_final: 0.7739 (m100) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1407 time to fit residues: 14.3597 Evaluate side-chains 78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4198 r_free = 0.4198 target = 0.172804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151981 restraints weight = 6351.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156512 restraints weight = 2960.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159443 restraints weight = 1712.685| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3041 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= 0.210 Angle : 0.701 15.062 5353 Z= 0.347 Chirality : 0.041 0.175 619 Planarity : 0.004 0.037 660 Dihedral : 4.305 17.771 536 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer: Outliers : 3.23 % Allowed : 21.09 % 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: 1.52 (0.40), residues: 479 helix: 1.81 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.26 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 71 HIS 0.002 0.001 HIS A 137 PHE 0.028 0.002 PHE A 34 TYR 0.033 0.002 TYR A 284 ARG 0.003 0.000 ARG A 128 ********************** 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 80 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.5438 (OUTLIER) cc_final: 0.5039 (m-10) REVERT: A 131 TRP cc_start: 0.7979 (m100) cc_final: 0.7736 (m100) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.1453 time to fit residues: 14.2308 Evaluate side-chains 80 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 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 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 246 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 363 VAL 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: 0.6980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 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 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 = 0.4183 r_free = 0.4183 target = 0.171288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150816 restraints weight = 6255.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155257 restraints weight = 2905.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158108 restraints weight = 1677.091| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3933 Z= 0.239 Angle : 0.717 15.026 5353 Z= 0.361 Chirality : 0.041 0.161 619 Planarity : 0.005 0.037 660 Dihedral : 4.384 17.935 536 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.38 % Favored : 95.20 % Rotamer: Outliers : 2.73 % Allowed : 22.33 % Favored : 74.94 % 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: 1.40 (0.40), residues: 479 helix: 1.65 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.16 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 71 HIS 0.002 0.001 HIS A 137 PHE 0.030 0.002 PHE A 34 TYR 0.052 0.002 TYR A 284 ARG 0.003 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.69 seconds wall clock time: 29 minutes 18.77 seconds (1758.77 seconds total)