Starting phenix.real_space_refine on Sun Apr 27 11:13:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362.map" model { file = "/net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jce_61362/04_2025/9jce_61362_neut.cif" } resolution = 3.59 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= 0.013 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 31 5.16 5 C 3463 2.51 5 N 976 2.21 5 O 1041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4933 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 533 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Time building chain proxies: 9.42, per 1000 atoms: 1.71 Number of scatterers: 5511 At special positions: 0 Unit cell: (85.28, 104.14, 113.98, 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 31 16.00 O 1041 8.00 N 976 7.00 C 3463 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: 1.53 Conformation dependent library (CDL) restraints added in 696.0 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 1 sheets defined 69.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.525A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.698A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 37 removed outlier: 4.031A pdb=" N TYR A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.562A pdb=" N VAL A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.596A pdb=" N VAL A 104 " --> pdb=" O HIS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.956A pdb=" N VAL A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.875A pdb=" N ILE A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 246 through 261 removed outlier: 3.608A pdb=" N ALA A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 320 through 337 removed outlier: 3.951A pdb=" N MET A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.730A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.556A pdb=" N CYS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.553A pdb=" N LEU A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 428 Processing helix chain 'A' and resid 432 through 456 Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.542A pdb=" N GLY A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 596 through 609 Processing helix chain 'A' and resid 617 through 627 removed outlier: 3.675A pdb=" N GLY A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'B' and resid 63 through 84 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.662A pdb=" N THR B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.502A pdb=" N SER A 47 " --> pdb=" O SER A 40 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 909 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: 1.47 Time building geometry restraints manager: 1.66 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: 1864 1.34 - 1.46: 655 1.46 - 1.57: 3042 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5605 Sorted by residual: bond pdb=" C PRO B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" CG LEU A 329 " pdb=" CD2 LEU A 329 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.66e-01 bond pdb=" C ALA A 21 " pdb=" N ALA A 22 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 8.11e-01 bond pdb=" CA PRO B 116 " pdb=" C PRO B 116 " ideal model delta sigma weight residual 1.517 1.525 -0.008 9.30e-03 1.16e+04 7.54e-01 bond pdb=" C LEU B 126 " pdb=" N PRO B 127 " ideal model delta sigma weight residual 1.335 1.345 -0.011 1.28e-02 6.10e+03 7.00e-01 ... (remaining 5600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 7392 1.54 - 3.08: 176 3.08 - 4.62: 26 4.62 - 6.16: 6 6.16 - 7.70: 1 Bond angle restraints: 7601 Sorted by residual: angle pdb=" C PHE B 69 " pdb=" N PHE B 70 " pdb=" CA PHE B 70 " ideal model delta sigma weight residual 121.14 115.97 5.17 1.75e+00 3.27e-01 8.73e+00 angle pdb=" C THR A 189 " pdb=" N ALA A 190 " pdb=" CA ALA A 190 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.06e+00 angle pdb=" N PRO B 116 " pdb=" CA PRO B 116 " pdb=" C PRO B 116 " ideal model delta sigma weight residual 110.70 114.08 -3.38 1.22e+00 6.72e-01 7.69e+00 angle pdb=" CA PRO B 116 " pdb=" C PRO B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 117.93 121.19 -3.26 1.20e+00 6.94e-01 7.36e+00 angle pdb=" C ASN A 357 " pdb=" N MET A 358 " pdb=" CA MET A 358 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 7596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 2976 17.25 - 34.51: 339 34.51 - 51.76: 64 51.76 - 69.02: 15 69.02 - 86.27: 5 Dihedral angle restraints: 3399 sinusoidal: 1338 harmonic: 2061 Sorted by residual: dihedral pdb=" CA HIS A 110 " pdb=" C HIS A 110 " pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP A 322 " pdb=" CB ASP A 322 " pdb=" CG ASP A 322 " pdb=" OD1 ASP A 322 " ideal model delta sinusoidal sigma weight residual -30.00 -88.62 58.62 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CG ARG A 603 " pdb=" CD ARG A 603 " pdb=" NE ARG A 603 " pdb=" CZ ARG A 603 " ideal model delta sinusoidal sigma weight residual 90.00 134.48 -44.48 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 787 0.067 - 0.135: 89 0.135 - 0.202: 4 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 881 Sorted by residual: chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA PHE A 626 " pdb=" N PHE A 626 " pdb=" C PHE A 626 " pdb=" CB PHE A 626 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB ILE A 200 " pdb=" CA ILE A 200 " pdb=" CG1 ILE A 200 " pdb=" CG2 ILE A 200 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 878 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 616 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO A 617 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 124 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " 0.016 2.00e-02 2.50e+03 1.30e-02 2.96e+00 pdb=" CG PHE B 70 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " 0.002 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1100 2.77 - 3.31: 5445 3.31 - 3.84: 9482 3.84 - 4.37: 10642 4.37 - 4.90: 18271 Nonbonded interactions: 44940 Sorted by model distance: nonbonded pdb=" OH TYR A 449 " pdb=" O PRO A 497 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP A 499 " pdb=" OG1 THR A 503 " model vdw 2.296 3.040 nonbonded pdb=" O GLY A 377 " pdb=" NH1 ARG A 379 " model vdw 2.346 3.120 nonbonded pdb=" OD2 ASP A 567 " pdb=" NH2 ARG A 603 " model vdw 2.350 3.120 nonbonded pdb=" OG1 THR A 90 " pdb=" ND1 HIS A 116 " model vdw 2.356 3.120 ... (remaining 44935 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: 18.830 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.033 5605 Z= 0.162 Angle : 0.591 7.697 7601 Z= 0.327 Chirality : 0.043 0.337 881 Planarity : 0.005 0.055 991 Dihedral : 15.145 86.270 2063 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.31), residues: 691 helix: 0.00 (0.23), residues: 464 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.006 0.001 HIS A 627 PHE 0.029 0.002 PHE B 70 TYR 0.023 0.002 TYR A 542 ARG 0.002 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.13761 ( 307) hydrogen bonds : angle 5.43477 ( 909) covalent geometry : bond 0.00377 ( 5605) covalent geometry : angle 0.59083 ( 7601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7894 (t) cc_final: 0.7680 (t) REVERT: A 105 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7103 (tptt) REVERT: A 174 LEU cc_start: 0.8896 (mt) cc_final: 0.8652 (mp) REVERT: A 228 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7344 (tt0) REVERT: A 383 LYS cc_start: 0.8228 (mttt) cc_final: 0.7696 (mtmt) REVERT: A 417 GLU cc_start: 0.7801 (tp30) cc_final: 0.7580 (tp30) REVERT: A 437 MET cc_start: 0.8113 (tpp) cc_final: 0.7855 (tpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1979 time to fit residues: 35.0466 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 39 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS A 511 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130545 restraints weight = 8225.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133912 restraints weight = 4999.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136030 restraints weight = 3549.656| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5605 Z= 0.121 Angle : 0.537 7.227 7601 Z= 0.285 Chirality : 0.039 0.176 881 Planarity : 0.004 0.044 991 Dihedral : 4.025 30.301 761 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.68 % Allowed : 10.92 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.32), residues: 691 helix: 0.74 (0.24), residues: 477 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.003 0.001 HIS A 382 PHE 0.025 0.002 PHE A 626 TYR 0.018 0.001 TYR A 139 ARG 0.005 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 307) hydrogen bonds : angle 3.86189 ( 909) covalent geometry : bond 0.00273 ( 5605) covalent geometry : angle 0.53707 ( 7601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 56 ASN cc_start: 0.8027 (m-40) cc_final: 0.7827 (m110) REVERT: A 105 LYS cc_start: 0.7551 (mmmm) cc_final: 0.7109 (tptt) REVERT: A 228 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7064 (tt0) REVERT: A 417 GLU cc_start: 0.7943 (tp30) cc_final: 0.7522 (tp30) REVERT: A 437 MET cc_start: 0.8131 (tpp) cc_final: 0.7826 (tpp) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.1771 time to fit residues: 24.0042 Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.162495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129414 restraints weight = 8373.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131904 restraints weight = 5288.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132614 restraints weight = 3999.094| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5605 Z= 0.159 Angle : 0.541 7.191 7601 Z= 0.288 Chirality : 0.040 0.148 881 Planarity : 0.004 0.040 991 Dihedral : 3.954 23.599 761 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.52 % Allowed : 12.44 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.32), residues: 691 helix: 1.02 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 209 HIS 0.004 0.001 HIS A 199 PHE 0.025 0.002 PHE A 626 TYR 0.013 0.001 TYR A 542 ARG 0.005 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 307) hydrogen bonds : angle 3.76296 ( 909) covalent geometry : bond 0.00376 ( 5605) covalent geometry : angle 0.54134 ( 7601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7830 (mt) cc_final: 0.7609 (mp) REVERT: A 105 LYS cc_start: 0.7633 (mmmm) cc_final: 0.7227 (tptt) REVERT: A 383 LYS cc_start: 0.8389 (mttt) cc_final: 0.8084 (mtmt) REVERT: A 417 GLU cc_start: 0.7946 (tp30) cc_final: 0.7501 (tp30) REVERT: A 437 MET cc_start: 0.8160 (tpp) cc_final: 0.7873 (tpp) outliers start: 15 outliers final: 14 residues processed: 94 average time/residue: 0.1800 time to fit residues: 22.4061 Evaluate side-chains 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127103 restraints weight = 8479.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130421 restraints weight = 5234.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132653 restraints weight = 3783.810| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5605 Z= 0.173 Angle : 0.538 6.977 7601 Z= 0.286 Chirality : 0.040 0.140 881 Planarity : 0.004 0.040 991 Dihedral : 3.949 16.449 761 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.86 % Allowed : 14.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.32), residues: 691 helix: 1.22 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 199 PHE 0.025 0.002 PHE A 626 TYR 0.016 0.001 TYR A 542 ARG 0.005 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 307) hydrogen bonds : angle 3.70695 ( 909) covalent geometry : bond 0.00411 ( 5605) covalent geometry : angle 0.53809 ( 7601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.637 Fit side-chains REVERT: A 74 GLN cc_start: 0.8667 (pm20) cc_final: 0.8300 (pm20) REVERT: A 105 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7211 (tptt) REVERT: A 121 ASN cc_start: 0.8059 (t0) cc_final: 0.7712 (t0) REVERT: A 383 LYS cc_start: 0.8410 (mttt) cc_final: 0.8087 (mtmt) REVERT: A 437 MET cc_start: 0.8099 (tpp) cc_final: 0.7776 (tpp) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.1668 time to fit residues: 21.8978 Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 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 = 0.3910 r_free = 0.3910 target = 0.160321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128501 restraints weight = 8230.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129473 restraints weight = 5217.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130623 restraints weight = 4275.608| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5605 Z= 0.151 Angle : 0.526 6.842 7601 Z= 0.282 Chirality : 0.040 0.214 881 Planarity : 0.004 0.052 991 Dihedral : 3.955 15.929 761 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.19 % Allowed : 15.97 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.32), residues: 691 helix: 1.37 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.004 0.001 HIS A 199 PHE 0.022 0.002 PHE A 626 TYR 0.012 0.001 TYR A 542 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 307) hydrogen bonds : angle 3.65828 ( 909) covalent geometry : bond 0.00355 ( 5605) covalent geometry : angle 0.52582 ( 7601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.656 Fit side-chains REVERT: A 74 GLN cc_start: 0.8637 (pm20) cc_final: 0.8280 (pm20) REVERT: A 105 LYS cc_start: 0.7618 (mmmm) cc_final: 0.7294 (tptt) REVERT: A 121 ASN cc_start: 0.8047 (t0) cc_final: 0.7684 (t0) REVERT: A 139 TYR cc_start: 0.8149 (t80) cc_final: 0.7835 (t80) REVERT: A 437 MET cc_start: 0.8186 (tpp) cc_final: 0.7831 (tpp) REVERT: A 529 ASP cc_start: 0.7901 (p0) cc_final: 0.7690 (p0) outliers start: 19 outliers final: 17 residues processed: 91 average time/residue: 0.1601 time to fit residues: 19.6092 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 382 HIS ** A 511 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 = 0.3915 r_free = 0.3915 target = 0.160977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128773 restraints weight = 8174.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130600 restraints weight = 5280.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131102 restraints weight = 3975.104| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5605 Z= 0.161 Angle : 0.536 6.763 7601 Z= 0.285 Chirality : 0.041 0.220 881 Planarity : 0.004 0.059 991 Dihedral : 3.975 15.549 761 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.87 % Allowed : 17.14 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.32), residues: 691 helix: 1.43 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.009 0.001 HIS A 382 PHE 0.023 0.002 PHE A 626 TYR 0.010 0.001 TYR A 542 ARG 0.002 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 307) hydrogen bonds : angle 3.62779 ( 909) covalent geometry : bond 0.00378 ( 5605) covalent geometry : angle 0.53625 ( 7601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.612 Fit side-chains REVERT: A 105 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7299 (tptt) REVERT: A 121 ASN cc_start: 0.8079 (t0) cc_final: 0.7693 (t0) REVERT: A 139 TYR cc_start: 0.8133 (t80) cc_final: 0.7822 (t80) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.1502 time to fit residues: 19.9385 Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.2980 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.169921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137350 restraints weight = 7953.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140945 restraints weight = 4727.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143251 restraints weight = 3320.493| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5605 Z= 0.130 Angle : 0.518 6.677 7601 Z= 0.279 Chirality : 0.040 0.219 881 Planarity : 0.004 0.066 991 Dihedral : 3.943 19.001 761 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 17.31 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.15 (0.32), residues: 691 helix: 1.58 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 PHE 0.021 0.001 PHE A 626 TYR 0.010 0.001 TYR A 273 ARG 0.003 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 307) hydrogen bonds : angle 3.53152 ( 909) covalent geometry : bond 0.00304 ( 5605) covalent geometry : angle 0.51846 ( 7601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.589 Fit side-chains REVERT: A 105 LYS cc_start: 0.7616 (mmmm) cc_final: 0.7354 (tptt) REVERT: A 121 ASN cc_start: 0.8154 (t0) cc_final: 0.7773 (t0) REVERT: A 139 TYR cc_start: 0.8102 (t80) cc_final: 0.7822 (t80) outliers start: 23 outliers final: 19 residues processed: 94 average time/residue: 0.1461 time to fit residues: 18.6658 Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.0030 chunk 22 optimal weight: 0.0970 chunk 44 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 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 = 0.4012 r_free = 0.4012 target = 0.169190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136781 restraints weight = 7948.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140429 restraints weight = 4614.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142790 restraints weight = 3192.553| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5605 Z= 0.119 Angle : 0.511 6.613 7601 Z= 0.274 Chirality : 0.039 0.224 881 Planarity : 0.004 0.070 991 Dihedral : 3.846 16.242 761 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.70 % Allowed : 17.98 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.20 (0.32), residues: 691 helix: 1.57 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 PHE 0.019 0.001 PHE A 626 TYR 0.009 0.001 TYR A 273 ARG 0.011 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 307) hydrogen bonds : angle 3.43920 ( 909) covalent geometry : bond 0.00276 ( 5605) covalent geometry : angle 0.51107 ( 7601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.957 Fit side-chains REVERT: A 105 LYS cc_start: 0.7607 (mmmm) cc_final: 0.7368 (tptt) REVERT: A 121 ASN cc_start: 0.8136 (t0) cc_final: 0.7744 (t0) REVERT: A 139 TYR cc_start: 0.8084 (t80) cc_final: 0.7785 (t80) outliers start: 22 outliers final: 20 residues processed: 93 average time/residue: 0.2413 time to fit residues: 31.7549 Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 chunk 17 optimal weight: 0.4980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 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 = 0.4020 r_free = 0.4020 target = 0.170498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138365 restraints weight = 8128.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140203 restraints weight = 5050.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140384 restraints weight = 3741.518| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5605 Z= 0.123 Angle : 0.552 8.204 7601 Z= 0.294 Chirality : 0.040 0.216 881 Planarity : 0.005 0.073 991 Dihedral : 3.836 16.346 761 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.70 % Allowed : 18.66 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.32 (0.32), residues: 691 helix: 1.66 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 209 HIS 0.009 0.001 HIS A 382 PHE 0.019 0.001 PHE A 626 TYR 0.009 0.001 TYR A 273 ARG 0.009 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 307) hydrogen bonds : angle 3.42701 ( 909) covalent geometry : bond 0.00289 ( 5605) covalent geometry : angle 0.55216 ( 7601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.644 Fit side-chains REVERT: A 105 LYS cc_start: 0.7629 (mmmm) cc_final: 0.7345 (tptt) REVERT: A 121 ASN cc_start: 0.8114 (t0) cc_final: 0.7715 (t0) REVERT: A 139 TYR cc_start: 0.8074 (t80) cc_final: 0.7813 (t80) outliers start: 22 outliers final: 21 residues processed: 89 average time/residue: 0.1563 time to fit residues: 18.9153 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 20 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 511 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 = 0.3970 r_free = 0.3970 target = 0.164917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133750 restraints weight = 8060.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135491 restraints weight = 5202.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136205 restraints weight = 3758.018| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5605 Z= 0.204 Angle : 0.617 7.604 7601 Z= 0.325 Chirality : 0.042 0.221 881 Planarity : 0.005 0.069 991 Dihedral : 4.100 19.907 761 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.03 % Allowed : 19.16 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.01 (0.32), residues: 691 helix: 1.38 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 PHE 0.023 0.002 PHE A 626 TYR 0.010 0.001 TYR A 273 ARG 0.007 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 307) hydrogen bonds : angle 3.69756 ( 909) covalent geometry : bond 0.00491 ( 5605) covalent geometry : angle 0.61706 ( 7601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.586 Fit side-chains REVERT: A 105 LYS cc_start: 0.7732 (mmmm) cc_final: 0.7411 (tptt) REVERT: A 121 ASN cc_start: 0.8166 (t0) cc_final: 0.7839 (t0) REVERT: A 398 LEU cc_start: 0.9223 (mm) cc_final: 0.8870 (mp) outliers start: 24 outliers final: 20 residues processed: 87 average time/residue: 0.1691 time to fit residues: 20.3695 Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 7 optimal weight: 0.0020 chunk 66 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 25 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 overall best weight: 0.1286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 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 = 0.3882 r_free = 0.3882 target = 0.161089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131310 restraints weight = 7981.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132071 restraints weight = 6133.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132686 restraints weight = 4595.068| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5605 Z= 0.115 Angle : 0.561 7.742 7601 Z= 0.299 Chirality : 0.039 0.212 881 Planarity : 0.004 0.070 991 Dihedral : 3.922 20.717 761 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.03 % Allowed : 20.50 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.31 (0.32), residues: 691 helix: 1.61 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 209 HIS 0.008 0.001 HIS A 382 PHE 0.020 0.002 PHE A 626 TYR 0.014 0.001 TYR A 139 ARG 0.007 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 307) hydrogen bonds : angle 3.44933 ( 909) covalent geometry : bond 0.00266 ( 5605) covalent geometry : angle 0.56105 ( 7601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.47 seconds wall clock time: 58 minutes 51.49 seconds (3531.49 seconds total)