Starting phenix.real_space_refine on Tue Feb 11 06:54:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.map" model { file = "/net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pdd_13334/02_2025/7pdd_13334.cif" } resolution = 4.2 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 33 5.16 5 C 2847 2.51 5 N 772 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3550 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Time building chain proxies: 3.35, per 1000 atoms: 0.74 Number of scatterers: 4516 At special positions: 0 Unit cell: (94.77, 77.76, 79.38, 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 33 16.00 O 864 8.00 N 772 7.00 C 2847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.12 Conformation dependent library (CDL) restraints added in 514.0 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 50.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.552A pdb=" N LYS A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.694A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.602A pdb=" N MET A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.779A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1038 through 1047 Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 3.699A pdb=" N PHE A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1097 removed outlier: 3.912A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1157 removed outlier: 3.878A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 4.280A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1219 removed outlier: 3.625A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 532 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 492 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.182A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN A1208 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1166 " --> pdb=" O GLN A1208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1241 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 756 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: 1.30 Time building geometry restraints manager: 1.31 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: 1515 1.34 - 1.46: 976 1.46 - 1.58: 2050 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 4595 Sorted by residual: bond pdb=" N ASP A 541 " pdb=" CA ASP A 541 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.69e+00 bond pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.29e-02 6.01e+03 1.11e+00 bond pdb=" CA ASN A1035 " pdb=" C ASN A1035 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.24e-02 6.50e+03 8.21e-01 bond pdb=" C GLU A 453 " pdb=" O GLU A 453 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.66e-01 ... (remaining 4590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 5935 1.58 - 3.15: 212 3.15 - 4.73: 33 4.73 - 6.30: 6 6.30 - 7.88: 3 Bond angle restraints: 6189 Sorted by residual: angle pdb=" N TYR A 446 " pdb=" CA TYR A 446 " pdb=" C TYR A 446 " ideal model delta sigma weight residual 108.79 113.27 -4.48 1.53e+00 4.27e-01 8.58e+00 angle pdb=" C TYR A 445 " pdb=" N TYR A 446 " pdb=" CA TYR A 446 " ideal model delta sigma weight residual 121.62 116.31 5.31 1.83e+00 2.99e-01 8.43e+00 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 121.97 117.45 4.52 1.80e+00 3.09e-01 6.29e+00 angle pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 110.44 113.29 -2.85 1.20e+00 6.94e-01 5.63e+00 angle pdb=" C THR A1181 " pdb=" N LYS A1182 " pdb=" CA LYS A1182 " ideal model delta sigma weight residual 122.39 126.25 -3.86 1.64e+00 3.72e-01 5.54e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2448 17.24 - 34.48: 248 34.48 - 51.72: 44 51.72 - 68.96: 7 68.96 - 86.20: 5 Dihedral angle restraints: 2752 sinusoidal: 1102 harmonic: 1650 Sorted by residual: dihedral pdb=" CA THR A1180 " pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 321 " pdb=" C LYS A 321 " pdb=" N ASP A 322 " pdb=" CA ASP A 322 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.059: 186 0.059 - 0.088: 78 0.088 - 0.117: 29 0.117 - 0.146: 4 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA ASP A 541 " pdb=" N ASP A 541 " pdb=" C ASP A 541 " pdb=" CB ASP A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL A 509 " pdb=" N VAL A 509 " pdb=" C VAL A 509 " pdb=" CB VAL A 509 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 677 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A1038 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1072 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TYR A1072 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A1072 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A1073 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 453 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 454 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.017 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 95 2.65 - 3.22: 4861 3.22 - 3.78: 7361 3.78 - 4.34: 9956 4.34 - 4.90: 15254 Nonbonded interactions: 37527 Sorted by model distance: nonbonded pdb=" O SER A 532 " pdb=" OG1 THR A 535 " model vdw 2.092 3.040 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A1226 " pdb=" OG1 THR A1229 " model vdw 2.153 3.040 nonbonded pdb=" O SER A1196 " pdb=" OG1 THR A1200 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A1206 " pdb=" O PRO A1244 " model vdw 2.222 3.120 ... (remaining 37522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.050 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.004 0.044 4595 Z= 0.254 Angle : 0.748 7.879 6189 Z= 0.445 Chirality : 0.042 0.146 680 Planarity : 0.004 0.048 803 Dihedral : 14.377 86.204 1694 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -4.11 (0.29), residues: 567 helix: -2.34 (0.25), residues: 273 sheet: -2.54 (0.40), residues: 105 loop : -3.08 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1031 HIS 0.005 0.002 HIS A1170 PHE 0.010 0.002 PHE A1224 TYR 0.015 0.002 TYR A1241 ARG 0.003 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8592 (m-10) cc_final: 0.8227 (m-80) REVERT: A 425 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8453 (mtp180) REVERT: A 429 LEU cc_start: 0.9525 (tp) cc_final: 0.9280 (tt) REVERT: B 56 TRP cc_start: 0.7689 (t60) cc_final: 0.7441 (t-100) REVERT: B 114 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8269 (mmtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2150 time to fit residues: 35.3324 Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 HIS A1154 ASN A1237 GLN B 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.096817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075194 restraints weight = 17467.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.077248 restraints weight = 12122.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.078694 restraints weight = 9309.889| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4595 Z= 0.200 Angle : 0.677 7.255 6189 Z= 0.360 Chirality : 0.044 0.152 680 Planarity : 0.004 0.056 803 Dihedral : 5.238 24.604 615 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.31), residues: 567 helix: -0.82 (0.28), residues: 280 sheet: -2.08 (0.43), residues: 105 loop : -2.40 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1159 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.002 PHE A1168 TYR 0.019 0.002 TYR A 446 ARG 0.005 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.8385 (m-10) cc_final: 0.8185 (m-10) REVERT: A 423 PHE cc_start: 0.8811 (m-10) cc_final: 0.8395 (m-80) REVERT: A 425 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8287 (mtp180) REVERT: A 510 TRP cc_start: 0.7012 (m-90) cc_final: 0.6724 (m-90) REVERT: A 520 MET cc_start: 0.7356 (ttm) cc_final: 0.7043 (mtp) REVERT: A 543 TYR cc_start: 0.7542 (m-80) cc_final: 0.6885 (m-80) REVERT: A 1075 ASN cc_start: 0.7966 (m-40) cc_final: 0.7589 (p0) REVERT: A 1081 GLU cc_start: 0.7821 (tp30) cc_final: 0.7595 (tp30) REVERT: A 1084 ARG cc_start: 0.8916 (mtt90) cc_final: 0.8074 (mtt-85) REVERT: A 1141 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8627 (mm-30) REVERT: A 1146 MET cc_start: 0.9058 (ppp) cc_final: 0.8807 (ppp) REVERT: B 56 TRP cc_start: 0.7892 (t60) cc_final: 0.7620 (t-100) REVERT: B 112 PHE cc_start: 0.7231 (m-80) cc_final: 0.6997 (m-80) REVERT: B 114 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7997 (mmtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1947 time to fit residues: 32.6797 Evaluate side-chains 107 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.095748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.076754 restraints weight = 17793.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.078157 restraints weight = 10662.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.079208 restraints weight = 8670.182| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4595 Z= 0.200 Angle : 0.648 8.402 6189 Z= 0.345 Chirality : 0.043 0.149 680 Planarity : 0.004 0.055 803 Dihedral : 5.096 24.179 615 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: -1.78 (0.33), residues: 567 helix: -0.19 (0.29), residues: 281 sheet: -1.73 (0.45), residues: 105 loop : -2.21 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1159 HIS 0.003 0.001 HIS A1170 PHE 0.011 0.001 PHE A1168 TYR 0.020 0.002 TYR A 446 ARG 0.002 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.8679 (tt) cc_final: 0.8210 (tt) REVERT: A 423 PHE cc_start: 0.8865 (m-10) cc_final: 0.8329 (m-80) REVERT: A 520 MET cc_start: 0.7425 (ttm) cc_final: 0.6863 (tpp) REVERT: A 1075 ASN cc_start: 0.8039 (m-40) cc_final: 0.7678 (p0) REVERT: A 1084 ARG cc_start: 0.8882 (mtt90) cc_final: 0.8152 (mtt-85) REVERT: A 1141 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8911 (mm-30) REVERT: A 1146 MET cc_start: 0.9030 (ppp) cc_final: 0.8748 (ppp) REVERT: A 1198 MET cc_start: 0.8718 (mtp) cc_final: 0.8351 (ppp) REVERT: B 16 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8717 (mmtm) REVERT: B 112 PHE cc_start: 0.7231 (m-80) cc_final: 0.6950 (m-80) REVERT: B 114 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8149 (mmtt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1930 time to fit residues: 30.3874 Evaluate side-chains 93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 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 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** 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 = 0.4001 r_free = 0.4001 target = 0.098495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.076967 restraints weight = 17704.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.078980 restraints weight = 12248.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.080386 restraints weight = 9399.698| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4595 Z= 0.184 Angle : 0.647 7.092 6189 Z= 0.346 Chirality : 0.043 0.148 680 Planarity : 0.004 0.053 803 Dihedral : 4.890 23.932 615 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.34), residues: 567 helix: -0.17 (0.29), residues: 285 sheet: -1.30 (0.47), residues: 105 loop : -2.02 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 56 HIS 0.005 0.001 HIS A 530 PHE 0.011 0.001 PHE A1168 TYR 0.020 0.002 TYR A 446 ARG 0.007 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8842 (m-10) cc_final: 0.8284 (m-80) REVERT: A 1075 ASN cc_start: 0.7981 (m-40) cc_final: 0.7681 (p0) REVERT: A 1141 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8365 (mm-30) REVERT: A 1146 MET cc_start: 0.9055 (ppp) cc_final: 0.8731 (ppp) REVERT: A 1198 MET cc_start: 0.8655 (mtp) cc_final: 0.8379 (ppp) REVERT: B 112 PHE cc_start: 0.7205 (m-80) cc_final: 0.6948 (m-80) REVERT: B 114 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8113 (mmtt) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1980 time to fit residues: 30.5935 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.097623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.076592 restraints weight = 18483.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.078322 restraints weight = 13542.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.079561 restraints weight = 10747.559| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.213 Angle : 0.709 9.401 6189 Z= 0.375 Chirality : 0.043 0.156 680 Planarity : 0.004 0.051 803 Dihedral : 4.996 23.432 615 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.33), residues: 567 helix: -0.26 (0.29), residues: 285 sheet: -1.15 (0.50), residues: 99 loop : -2.07 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 56 HIS 0.005 0.001 HIS A 530 PHE 0.009 0.001 PHE A1168 TYR 0.013 0.002 TYR A1083 ARG 0.004 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8647 (m-10) cc_final: 0.8171 (m-80) REVERT: A 1084 ARG cc_start: 0.8752 (mtt90) cc_final: 0.8029 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 68 LYS cc_start: 0.8263 (mttt) cc_final: 0.7833 (mmtt) REVERT: B 112 PHE cc_start: 0.7208 (m-80) cc_final: 0.6987 (m-80) REVERT: B 114 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8122 (mmtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1979 time to fit residues: 29.2094 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.0770 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** 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 = 0.4008 r_free = 0.4008 target = 0.099074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.077558 restraints weight = 17690.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.079513 restraints weight = 12431.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.080929 restraints weight = 9591.714| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4595 Z= 0.183 Angle : 0.687 10.570 6189 Z= 0.360 Chirality : 0.044 0.160 680 Planarity : 0.004 0.048 803 Dihedral : 4.888 23.299 615 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.21 % Allowed : 2.08 % Favored : 97.71 % 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: -1.44 (0.34), residues: 567 helix: -0.13 (0.29), residues: 283 sheet: -1.04 (0.50), residues: 99 loop : -2.04 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 56 HIS 0.004 0.001 HIS A 530 PHE 0.009 0.001 PHE A1168 TYR 0.011 0.002 TYR A1083 ARG 0.006 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8702 (m-10) cc_final: 0.8175 (m-80) REVERT: A 1084 ARG cc_start: 0.8850 (mtt90) cc_final: 0.8105 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 1198 MET cc_start: 0.8352 (ppp) cc_final: 0.7870 (ppp) REVERT: B 64 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9160 (pm20) REVERT: B 68 LYS cc_start: 0.8268 (mttt) cc_final: 0.7863 (mmtt) REVERT: B 112 PHE cc_start: 0.7257 (m-80) cc_final: 0.7016 (m-80) REVERT: B 114 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8170 (mmtt) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1789 time to fit residues: 26.5420 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 8.9990 chunk 54 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.095787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.074461 restraints weight = 18033.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076253 restraints weight = 12966.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.077531 restraints weight = 10182.762| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4595 Z= 0.289 Angle : 0.771 11.064 6189 Z= 0.410 Chirality : 0.046 0.220 680 Planarity : 0.004 0.050 803 Dihedral : 5.208 23.659 615 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 (0.33), residues: 567 helix: -0.29 (0.29), residues: 283 sheet: -1.08 (0.50), residues: 99 loop : -2.14 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP B 56 HIS 0.006 0.002 HIS A 335 PHE 0.014 0.002 PHE A1093 TYR 0.016 0.002 TYR A1083 ARG 0.011 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8696 (m-10) cc_final: 0.8167 (m-80) REVERT: A 469 MET cc_start: 0.8686 (mmp) cc_final: 0.8455 (mmm) REVERT: A 1084 ARG cc_start: 0.8782 (mtt90) cc_final: 0.8209 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 68 LYS cc_start: 0.8282 (mttt) cc_final: 0.7935 (mmtt) REVERT: B 130 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8712 (mm-30) REVERT: B 133 GLN cc_start: 0.9216 (mp10) cc_final: 0.8899 (mp10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1904 time to fit residues: 27.2785 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** 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 = 0.3974 r_free = 0.3974 target = 0.097311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075875 restraints weight = 17705.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077710 restraints weight = 12828.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.079034 restraints weight = 10075.511| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.213 Angle : 0.752 11.207 6189 Z= 0.392 Chirality : 0.046 0.168 680 Planarity : 0.004 0.049 803 Dihedral : 5.054 22.295 615 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -1.43 (0.34), residues: 567 helix: -0.21 (0.29), residues: 284 sheet: -0.87 (0.51), residues: 99 loop : -1.98 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.015 0.001 PHE A1142 TYR 0.022 0.002 TYR A 446 ARG 0.011 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8584 (m-10) cc_final: 0.8086 (m-80) REVERT: A 469 MET cc_start: 0.8638 (mmp) cc_final: 0.8428 (mmm) REVERT: A 520 MET cc_start: 0.6772 (ttt) cc_final: 0.5713 (tmm) REVERT: A 1134 GLU cc_start: 0.8716 (pp20) cc_final: 0.7882 (pp20) REVERT: A 1141 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 68 LYS cc_start: 0.8240 (mttt) cc_final: 0.7911 (mmtt) REVERT: B 114 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8263 (mmtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1776 time to fit residues: 26.4843 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.098716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.077586 restraints weight = 17549.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079421 restraints weight = 12704.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080808 restraints weight = 9916.048| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.193 Angle : 0.728 11.673 6189 Z= 0.384 Chirality : 0.046 0.168 680 Planarity : 0.004 0.064 803 Dihedral : 4.977 24.229 615 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.34), residues: 567 helix: -0.14 (0.29), residues: 284 sheet: -0.83 (0.51), residues: 99 loop : -1.83 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 56 HIS 0.004 0.001 HIS A 530 PHE 0.018 0.001 PHE A1142 TYR 0.013 0.002 TYR A 446 ARG 0.011 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8758 (ttm) cc_final: 0.8383 (ttm) REVERT: A 423 PHE cc_start: 0.8543 (m-10) cc_final: 0.8006 (m-80) REVERT: A 425 ARG cc_start: 0.8752 (ptp-170) cc_final: 0.8469 (ptp-170) REVERT: A 509 VAL cc_start: 0.9317 (m) cc_final: 0.9086 (m) REVERT: A 520 MET cc_start: 0.6683 (ttt) cc_final: 0.5569 (tmm) REVERT: A 1084 ARG cc_start: 0.8482 (mtt90) cc_final: 0.8172 (mtt-85) REVERT: A 1134 GLU cc_start: 0.8703 (pp20) cc_final: 0.8172 (pp20) REVERT: A 1141 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 20 GLU cc_start: 0.9251 (mp0) cc_final: 0.8913 (pp20) REVERT: B 114 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8259 (mmtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1943 time to fit residues: 28.6261 Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.099918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.079030 restraints weight = 17880.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.080840 restraints weight = 13224.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.082147 restraints weight = 10395.583| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.195 Angle : 0.754 11.859 6189 Z= 0.395 Chirality : 0.046 0.171 680 Planarity : 0.004 0.065 803 Dihedral : 4.841 24.593 615 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.28 (0.34), residues: 567 helix: -0.13 (0.30), residues: 285 sheet: -0.92 (0.50), residues: 99 loop : -1.76 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.010 0.001 PHE A1160 TYR 0.014 0.001 TYR A 446 ARG 0.012 0.001 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8524 (m-10) cc_final: 0.7975 (m-80) REVERT: A 425 ARG cc_start: 0.8736 (ptp-170) cc_final: 0.8460 (ptp-170) REVERT: A 520 MET cc_start: 0.6578 (ttt) cc_final: 0.5491 (tmm) REVERT: A 569 TYR cc_start: 0.7969 (m-80) cc_final: 0.7683 (m-80) REVERT: A 1030 ASP cc_start: 0.8006 (t70) cc_final: 0.7638 (t0) REVERT: A 1084 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8139 (mtt-85) REVERT: A 1134 GLU cc_start: 0.8722 (pp20) cc_final: 0.8293 (pp20) REVERT: A 1141 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8500 (mm-30) REVERT: A 1146 MET cc_start: 0.8770 (ppp) cc_final: 0.8432 (ppp) REVERT: A 1190 ASP cc_start: 0.8397 (p0) cc_final: 0.7946 (p0) REVERT: A 1198 MET cc_start: 0.8098 (ppp) cc_final: 0.7672 (ppp) REVERT: B 20 GLU cc_start: 0.9257 (mp0) cc_final: 0.9001 (pp20) REVERT: B 114 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8261 (mmtt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1944 time to fit residues: 28.8141 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.098023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.077044 restraints weight = 17668.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.078795 restraints weight = 12912.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.080094 restraints weight = 10211.086| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4595 Z= 0.239 Angle : 0.747 11.938 6189 Z= 0.394 Chirality : 0.046 0.154 680 Planarity : 0.004 0.055 803 Dihedral : 5.012 25.736 615 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.33 (0.34), residues: 567 helix: -0.11 (0.30), residues: 284 sheet: -0.79 (0.56), residues: 76 loop : -1.91 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 56 HIS 0.009 0.001 HIS A 530 PHE 0.016 0.002 PHE A1142 TYR 0.012 0.002 TYR A 446 ARG 0.011 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.81 seconds wall clock time: 35 minutes 9.80 seconds (2109.80 seconds total)