Starting phenix.real_space_refine on Sat May 10 07:22:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jce_61362/05_2025/9jce_61362_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jce_61362/05_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_61362/05_2025/9jce_61362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jce_61362/05_2025/9jce_61362.map" model { file = "/net/cci-nas-00/data/ceres_data/9jce_61362/05_2025/9jce_61362_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jce_61362/05_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-5687/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: 8.92, per 1000 atoms: 1.62 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: 1.25 Conformation dependent library (CDL) restraints added in 627.0 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: 0.53 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: 1.45 Time building geometry restraints manager: 1.48 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: 22.670 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.600 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- 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 : 0.575 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: 0.1919 time to fit residues: 34.0238 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 : 0.724 ------------------------------------------------------------------------------- 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: 0.0980 chunk 39 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 overall best weight: 0.1980 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.163575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130445 restraints weight = 8217.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133893 restraints weight = 4934.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136064 restraints weight = 3496.742| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5605 Z= 0.122 Angle : 0.543 7.320 7601 Z= 0.288 Chirality : 0.039 0.206 881 Planarity : 0.004 0.045 991 Dihedral : 4.048 30.410 761 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.51 % Allowed : 11.26 % Favored : 87.23 % 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 : -0.85 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.004 0.001 HIS A 382 PHE 0.027 0.002 PHE A 626 TYR 0.019 0.001 TYR A 139 ARG 0.005 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 307) hydrogen bonds : angle 3.84477 ( 909) covalent geometry : bond 0.00270 ( 5605) covalent geometry : angle 0.54335 ( 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 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7117 (tptt) REVERT: A 417 GLU cc_start: 0.7961 (tp30) cc_final: 0.7511 (tp30) REVERT: A 437 MET cc_start: 0.8129 (tpp) cc_final: 0.7825 (tpp) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.1703 time to fit residues: 22.7082 Evaluate side-chains 87 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129898 restraints weight = 8354.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132387 restraints weight = 5277.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133103 restraints weight = 3844.556| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5605 Z= 0.150 Angle : 0.534 7.094 7601 Z= 0.284 Chirality : 0.040 0.149 881 Planarity : 0.004 0.040 991 Dihedral : 3.956 23.905 761 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.35 % Allowed : 12.77 % Favored : 84.87 % 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: 0.63 (0.32), residues: 691 helix: 1.03 (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 0.007 0.002 TRP A 209 HIS 0.004 0.001 HIS A 199 PHE 0.025 0.002 PHE A 626 TYR 0.014 0.001 TYR A 542 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 307) hydrogen bonds : angle 3.73770 ( 909) covalent geometry : bond 0.00352 ( 5605) covalent geometry : angle 0.53395 ( 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 104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7898 (mt) cc_final: 0.7691 (mp) REVERT: A 105 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7193 (tptt) REVERT: A 383 LYS cc_start: 0.8349 (mttt) cc_final: 0.8050 (mtmt) REVERT: A 417 GLU cc_start: 0.7952 (tp30) cc_final: 0.7485 (tp30) REVERT: A 437 MET cc_start: 0.8174 (tpp) cc_final: 0.7868 (tpp) outliers start: 14 outliers final: 13 residues processed: 98 average time/residue: 0.1656 time to fit residues: 21.5379 Evaluate side-chains 99 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.160989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127616 restraints weight = 8472.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130310 restraints weight = 5373.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130906 restraints weight = 3884.169| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2337 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 : 0.542 6.987 7601 Z= 0.288 Chirality : 0.040 0.135 881 Planarity : 0.004 0.040 991 Dihedral : 3.942 16.922 761 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.19 % Allowed : 14.12 % Favored : 82.69 % 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: 0.80 (0.32), residues: 691 helix: 1.23 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 225 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 0.024 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 0.03461 ( 307) hydrogen bonds : angle 3.71053 ( 909) covalent geometry : bond 0.00411 ( 5605) covalent geometry : angle 0.54234 ( 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 104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.652 Fit side-chains REVERT: A 24 LEU cc_start: 0.7886 (mt) cc_final: 0.7663 (mp) REVERT: A 105 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7229 (tptt) REVERT: A 121 ASN cc_start: 0.8023 (t0) cc_final: 0.7671 (t0) REVERT: A 383 LYS cc_start: 0.8409 (mttt) cc_final: 0.8093 (mtmt) REVERT: A 437 MET cc_start: 0.8194 (tpp) cc_final: 0.7831 (tpp) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.1730 time to fit residues: 22.1866 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 228 GLU 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 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 110 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: 0.0870 chunk 36 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138595 restraints weight = 8022.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140300 restraints weight = 4960.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140907 restraints weight = 3626.512| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2491 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= 0.120 Angle : 0.501 6.810 7601 Z= 0.270 Chirality : 0.039 0.208 881 Planarity : 0.004 0.057 991 Dihedral : 3.861 16.873 761 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.86 % Allowed : 16.97 % Favored : 80.17 % 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: 1.16 (0.33), residues: 691 helix: 1.53 (0.25), residues: 463 sheet: None (None), residues: 0 loop : -0.78 (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 0.019 0.001 PHE A 626 TYR 0.011 0.001 TYR A 139 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 307) hydrogen bonds : angle 3.56670 ( 909) covalent geometry : bond 0.00274 ( 5605) covalent geometry : angle 0.50117 ( 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 104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.629 Fit side-chains REVERT: A 105 LYS cc_start: 0.7657 (mmmm) cc_final: 0.7380 (tptt) REVERT: A 121 ASN cc_start: 0.8060 (t0) cc_final: 0.7685 (t0) REVERT: A 139 TYR cc_start: 0.8139 (t80) cc_final: 0.7833 (t80) REVERT: A 417 GLU cc_start: 0.7807 (tp30) cc_final: 0.7370 (tp30) REVERT: A 627 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.6844 (m-70) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1596 time to fit residues: 20.7077 Evaluate side-chains 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 56 ASN A 382 HIS ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128808 restraints weight = 8192.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130375 restraints weight = 5281.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130782 restraints weight = 4006.310| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5605 Z= 0.181 Angle : 0.551 6.783 7601 Z= 0.289 Chirality : 0.041 0.217 881 Planarity : 0.004 0.065 991 Dihedral : 3.971 17.038 761 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.87 % Allowed : 16.97 % Favored : 79.16 % 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: 0.97 (0.32), residues: 691 helix: 1.42 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.95 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.011 0.001 HIS A 382 PHE 0.023 0.002 PHE A 626 TYR 0.011 0.001 TYR A 542 ARG 0.004 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 307) hydrogen bonds : angle 3.63146 ( 909) covalent geometry : bond 0.00430 ( 5605) covalent geometry : angle 0.55059 ( 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 104 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.590 Fit side-chains REVERT: A 105 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7323 (tptt) REVERT: A 121 ASN cc_start: 0.8089 (t0) cc_final: 0.7707 (t0) REVERT: A 139 TYR cc_start: 0.8193 (t80) cc_final: 0.7855 (t80) REVERT: A 453 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8527 (mp) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.1478 time to fit residues: 19.5692 Evaluate side-chains 99 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 116 HIS 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 453 ILE 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 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.0770 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 0.0010 chunk 34 optimal weight: 0.9980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 146 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126613 restraints weight = 7781.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129149 restraints weight = 5217.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130899 restraints weight = 3935.156| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2800 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= 0.139 Angle : 0.523 6.692 7601 Z= 0.280 Chirality : 0.040 0.219 881 Planarity : 0.004 0.067 991 Dihedral : 3.975 18.070 761 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 17.82 % 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: 1.08 (0.32), residues: 691 helix: 1.52 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.94 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 209 HIS 0.012 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 0.03153 ( 307) hydrogen bonds : angle 3.52920 ( 909) covalent geometry : bond 0.00326 ( 5605) covalent geometry : angle 0.52338 ( 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 103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.640 Fit side-chains REVERT: A 105 LYS cc_start: 0.7695 (mmmm) cc_final: 0.7493 (tptt) REVERT: A 121 ASN cc_start: 0.8157 (t0) cc_final: 0.7804 (t0) REVERT: A 139 TYR cc_start: 0.8114 (t80) cc_final: 0.7861 (t80) REVERT: A 437 MET cc_start: 0.7895 (tpp) cc_final: 0.7636 (tpp) outliers start: 23 outliers final: 20 residues processed: 97 average time/residue: 0.1541 time to fit residues: 20.3708 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 : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 HIS 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 477 LEU 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 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 511 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 = 0.3820 r_free = 0.3820 target = 0.155833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124249 restraints weight = 7835.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126783 restraints weight = 5275.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128523 restraints weight = 3993.966| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2901 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= 0.181 Angle : 0.561 6.705 7601 Z= 0.298 Chirality : 0.041 0.230 881 Planarity : 0.004 0.069 991 Dihedral : 4.041 16.719 761 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.87 % Allowed : 17.82 % 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: 0.86 (0.32), residues: 691 helix: 1.30 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 209 HIS 0.011 0.001 HIS A 382 PHE 0.022 0.002 PHE A 626 TYR 0.010 0.001 TYR A 273 ARG 0.004 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 307) hydrogen bonds : angle 3.66215 ( 909) covalent geometry : bond 0.00433 ( 5605) covalent geometry : angle 0.56129 ( 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 97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.531 Fit side-chains REVERT: A 105 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7497 (tptt) REVERT: A 121 ASN cc_start: 0.8176 (t0) cc_final: 0.7868 (t0) REVERT: A 437 MET cc_start: 0.7924 (tpp) cc_final: 0.7653 (tpp) outliers start: 23 outliers final: 22 residues processed: 90 average time/residue: 0.1493 time to fit residues: 18.5929 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 HIS 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 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 619 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 511 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 = 0.3826 r_free = 0.3826 target = 0.156284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126953 restraints weight = 7848.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127270 restraints weight = 5665.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128008 restraints weight = 4653.869| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5605 Z= 0.168 Angle : 0.561 7.475 7601 Z= 0.297 Chirality : 0.041 0.221 881 Planarity : 0.004 0.072 991 Dihedral : 4.091 18.530 761 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.20 % Allowed : 18.99 % 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: 0.91 (0.32), residues: 691 helix: 1.30 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 PHE 0.022 0.002 PHE A 626 TYR 0.031 0.001 TYR A 139 ARG 0.004 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 307) hydrogen bonds : angle 3.64068 ( 909) covalent geometry : bond 0.00401 ( 5605) covalent geometry : angle 0.56057 ( 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 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.675 Fit side-chains REVERT: A 121 ASN cc_start: 0.8157 (t0) cc_final: 0.7840 (t0) REVERT: A 437 MET cc_start: 0.8074 (tpp) cc_final: 0.7775 (tpp) outliers start: 25 outliers final: 22 residues processed: 88 average time/residue: 0.1514 time to fit residues: 18.5690 Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 116 HIS 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 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 66 VAL 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 24 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 511 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 = 0.3812 r_free = 0.3812 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123245 restraints weight = 7911.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125745 restraints weight = 5341.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127499 restraints weight = 4062.083| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5605 Z= 0.199 Angle : 0.598 7.837 7601 Z= 0.314 Chirality : 0.042 0.222 881 Planarity : 0.004 0.072 991 Dihedral : 4.208 18.055 761 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.03 % Allowed : 19.33 % Favored : 76.64 % 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: 0.83 (0.32), residues: 691 helix: 1.19 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 209 HIS 0.011 0.001 HIS A 382 PHE 0.024 0.002 PHE A 626 TYR 0.011 0.001 TYR A 440 ARG 0.005 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 307) hydrogen bonds : angle 3.76397 ( 909) covalent geometry : bond 0.00477 ( 5605) covalent geometry : angle 0.59767 ( 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 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.644 Fit side-chains REVERT: A 105 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7055 (tptt) REVERT: A 359 GLU cc_start: 0.7620 (tp30) cc_final: 0.7097 (tp30) REVERT: A 437 MET cc_start: 0.8002 (tpp) cc_final: 0.7716 (tpp) outliers start: 24 outliers final: 24 residues processed: 88 average time/residue: 0.1535 time to fit residues: 18.5727 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 116 HIS 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 546 ILE 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 619 THR 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 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 121 ASN ** 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 = 0.3841 r_free = 0.3841 target = 0.157635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126028 restraints weight = 7888.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128662 restraints weight = 5294.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130406 restraints weight = 3982.527| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5605 Z= 0.142 Angle : 0.555 7.808 7601 Z= 0.295 Chirality : 0.040 0.218 881 Planarity : 0.004 0.069 991 Dihedral : 4.070 18.293 761 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 20.00 % Favored : 76.13 % 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: 1.07 (0.32), residues: 691 helix: 1.38 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.010 0.001 HIS A 382 PHE 0.022 0.002 PHE A 626 TYR 0.010 0.001 TYR A 273 ARG 0.005 0.000 ARG A 618 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 307) hydrogen bonds : angle 3.58316 ( 909) covalent geometry : bond 0.00338 ( 5605) covalent geometry : angle 0.55462 ( 7601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2950.14 seconds wall clock time: 52 minutes 54.06 seconds (3174.06 seconds total)