Starting phenix.real_space_refine on Wed Sep 17 05:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jce_61362/09_2025/9jce_61362_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jce_61362/09_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_61362/09_2025/9jce_61362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jce_61362/09_2025/9jce_61362.map" model { file = "/net/cci-nas-00/data/ceres_data/9jce_61362/09_2025/9jce_61362_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jce_61362/09_2025/9jce_61362_neut.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.24 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: 0.53 Conformation dependent library (CDL) restraints added in 246.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.16 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: 0.72 Time building geometry restraints manager: 0.69 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: 0.010 Normalize map: mean=0, sd=1: 18.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 321 TYR 0.023 0.002 TYR A 542 PHE 0.029 0.002 PHE B 70 TRP 0.006 0.001 TRP A 209 HIS 0.006 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5605) covalent geometry : angle 0.59083 ( 7601) hydrogen bonds : bond 0.13761 ( 307) hydrogen bonds : angle 5.43477 ( 909) *********************** 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 : 0.209 Fit side-chains revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7894 (t) cc_final: 0.7677 (t) REVERT: A 105 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7104 (tptt) REVERT: A 174 LEU cc_start: 0.8896 (mt) cc_final: 0.8651 (mp) REVERT: A 228 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7345 (tt0) REVERT: A 383 LYS cc_start: 0.8228 (mttt) cc_final: 0.7697 (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: 0.7856 (tpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0884 time to fit residues: 15.7390 Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 A 100 HIS A 511 ASN B 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124078 restraints weight = 8394.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125911 restraints weight = 5858.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126607 restraints weight = 4170.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127871 restraints weight = 3842.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127953 restraints weight = 3344.325| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1675 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= 0.157 Angle : 0.565 7.204 7601 Z= 0.299 Chirality : 0.040 0.192 881 Planarity : 0.004 0.043 991 Dihedral : 4.084 24.742 761 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.18 % Allowed : 10.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.32), residues: 691 helix: 0.67 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.019 0.001 TYR A 139 PHE 0.026 0.002 PHE B 70 TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5605) covalent geometry : angle 0.56531 ( 7601) hydrogen bonds : bond 0.03977 ( 307) hydrogen bonds : angle 4.03149 ( 909) *********************** 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 112 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 56 ASN cc_start: 0.8053 (m-40) cc_final: 0.7844 (m110) REVERT: A 105 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7105 (tptt) REVERT: A 174 LEU cc_start: 0.8999 (mt) cc_final: 0.8693 (mp) REVERT: A 228 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7143 (tt0) REVERT: A 230 CYS cc_start: 0.8009 (m) cc_final: 0.7691 (m) REVERT: A 383 LYS cc_start: 0.8308 (mttt) cc_final: 0.7901 (mtmt) REVERT: A 417 GLU cc_start: 0.8033 (tp30) cc_final: 0.7603 (tp30) REVERT: A 437 MET cc_start: 0.8264 (tpp) cc_final: 0.7848 (tpp) REVERT: A 495 ASN cc_start: 0.8120 (m-40) cc_final: 0.7884 (t0) REVERT: A 598 LYS cc_start: 0.7289 (ttmm) cc_final: 0.6986 (ttpp) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.0777 time to fit residues: 11.1682 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 560 VAL 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 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 57 optimal weight: 0.0980 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 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124726 restraints weight = 8256.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126061 restraints weight = 5707.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126616 restraints weight = 4243.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127689 restraints weight = 3995.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127926 restraints weight = 3419.548| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5605 Z= 0.140 Angle : 0.525 6.966 7601 Z= 0.280 Chirality : 0.039 0.144 881 Planarity : 0.004 0.042 991 Dihedral : 3.959 20.945 761 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.35 % Allowed : 12.27 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.32), residues: 691 helix: 1.05 (0.24), residues: 467 sheet: None (None), residues: 0 loop : -0.84 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.015 0.001 TYR A 542 PHE 0.023 0.002 PHE A 626 TRP 0.007 0.001 TRP A 209 HIS 0.006 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5605) covalent geometry : angle 0.52490 ( 7601) hydrogen bonds : bond 0.03524 ( 307) hydrogen bonds : angle 3.76744 ( 909) *********************** 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 106 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.223 Fit side-chains REVERT: A 74 GLN cc_start: 0.8621 (pm20) cc_final: 0.8175 (pm20) REVERT: A 105 LYS cc_start: 0.7560 (mmmm) cc_final: 0.7167 (tptt) REVERT: A 174 LEU cc_start: 0.9016 (mt) cc_final: 0.8722 (mp) REVERT: A 228 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 383 LYS cc_start: 0.8337 (mttt) cc_final: 0.7986 (mtmt) REVERT: A 417 GLU cc_start: 0.7986 (tp30) cc_final: 0.7529 (tp30) REVERT: A 437 MET cc_start: 0.8213 (tpp) cc_final: 0.7885 (tpp) REVERT: A 453 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 627 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7196 (m-70) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0797 time to fit residues: 10.7515 Evaluate side-chains 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 557 ILE Chi-restraints excluded: chain A residue 560 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 26 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 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123681 restraints weight = 8248.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125646 restraints weight = 5308.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126356 restraints weight = 4121.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126866 restraints weight = 3728.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127123 restraints weight = 3307.339| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2328 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= 0.184 Angle : 0.558 6.985 7601 Z= 0.293 Chirality : 0.040 0.143 881 Planarity : 0.004 0.042 991 Dihedral : 3.961 16.791 761 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.32), residues: 691 helix: 1.13 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.015 0.001 TYR A 542 PHE 0.024 0.002 PHE A 626 TRP 0.008 0.001 TRP A 209 HIS 0.006 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 5605) covalent geometry : angle 0.55772 ( 7601) hydrogen bonds : bond 0.03526 ( 307) hydrogen bonds : angle 3.79885 ( 909) *********************** 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 103 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.224 Fit side-chains REVERT: A 105 LYS cc_start: 0.7611 (mmmm) cc_final: 0.7244 (tptt) REVERT: A 139 TYR cc_start: 0.8195 (t80) cc_final: 0.7879 (t80) REVERT: A 228 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 383 LYS cc_start: 0.8411 (mttt) cc_final: 0.8165 (pttt) REVERT: A 437 MET cc_start: 0.8217 (tpp) cc_final: 0.7844 (tpp) REVERT: A 453 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 627 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7631 (m-70) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.0736 time to fit residues: 9.3775 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 315 GLU Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 511 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 627 HIS 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 18 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 36 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 495 ASN A 511 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.155942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124052 restraints weight = 8439.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125057 restraints weight = 6453.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126225 restraints weight = 4910.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126823 restraints weight = 4242.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126980 restraints weight = 3814.859| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2464 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= 0.130 Angle : 0.505 6.778 7601 Z= 0.271 Chirality : 0.038 0.131 881 Planarity : 0.004 0.042 991 Dihedral : 3.880 16.108 761 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.70 % Allowed : 14.62 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.32), residues: 691 helix: 1.37 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.015 0.001 TYR A 69 PHE 0.020 0.001 PHE A 626 TRP 0.007 0.001 TRP A 209 HIS 0.005 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5605) covalent geometry : angle 0.50523 ( 7601) hydrogen bonds : bond 0.03283 ( 307) hydrogen bonds : angle 3.62315 ( 909) *********************** 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 116 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.254 Fit side-chains REVERT: A 105 LYS cc_start: 0.7586 (mmmm) cc_final: 0.7250 (tptt) REVERT: A 139 TYR cc_start: 0.8168 (t80) cc_final: 0.7816 (t80) REVERT: A 174 LEU cc_start: 0.9022 (mt) cc_final: 0.8763 (mp) REVERT: A 228 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 383 LYS cc_start: 0.8410 (mttt) cc_final: 0.8137 (pttt) REVERT: A 417 GLU cc_start: 0.7923 (tp30) cc_final: 0.7442 (tp30) REVERT: A 437 MET cc_start: 0.8212 (tpp) cc_final: 0.7858 (tpp) REVERT: A 529 ASP cc_start: 0.7916 (p0) cc_final: 0.7715 (p0) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.0770 time to fit residues: 10.8818 Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 237 LEU 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 511 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 B residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.0170 chunk 49 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 382 HIS A 495 ASN A 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128163 restraints weight = 8142.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131529 restraints weight = 4780.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133671 restraints weight = 3380.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135216 restraints weight = 2650.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136147 restraints weight = 2230.310| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2620 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= 0.129 Angle : 0.516 6.687 7601 Z= 0.276 Chirality : 0.038 0.129 881 Planarity : 0.004 0.040 991 Dihedral : 3.909 16.644 761 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.70 % Allowed : 16.81 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.32), residues: 691 helix: 1.38 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.91 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 33 TYR 0.012 0.001 TYR A 69 PHE 0.021 0.001 PHE A 626 TRP 0.006 0.001 TRP A 209 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5605) covalent geometry : angle 0.51636 ( 7601) hydrogen bonds : bond 0.03198 ( 307) hydrogen bonds : angle 3.54090 ( 909) *********************** 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: 22 poor density : 82 time to evaluate : 0.215 Fit side-chains REVERT: A 105 LYS cc_start: 0.7580 (mmmm) cc_final: 0.7267 (tptt) REVERT: A 139 TYR cc_start: 0.8099 (t80) cc_final: 0.7758 (t80) outliers start: 22 outliers final: 19 residues processed: 94 average time/residue: 0.0692 time to fit residues: 8.9353 Evaluate side-chains 96 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 116 HIS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 511 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 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 59 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 511 ASN A 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129808 restraints weight = 8332.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132108 restraints weight = 5350.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132738 restraints weight = 3906.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133360 restraints weight = 3587.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133588 restraints weight = 3125.771| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2704 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= 0.144 Angle : 0.543 6.657 7601 Z= 0.287 Chirality : 0.041 0.390 881 Planarity : 0.004 0.039 991 Dihedral : 3.909 16.390 761 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.70 % Allowed : 17.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.32), residues: 691 helix: 1.34 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.010 0.001 TYR A 273 PHE 0.021 0.001 PHE A 626 TRP 0.005 0.001 TRP A 209 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5605) covalent geometry : angle 0.54292 ( 7601) hydrogen bonds : bond 0.03194 ( 307) hydrogen bonds : angle 3.56223 ( 909) *********************** 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 97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.214 Fit side-chains REVERT: A 105 LYS cc_start: 0.7631 (mmmm) cc_final: 0.7313 (tptt) REVERT: A 139 TYR cc_start: 0.8108 (t80) cc_final: 0.7774 (t80) outliers start: 22 outliers final: 19 residues processed: 88 average time/residue: 0.0728 time to fit residues: 8.7576 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 237 LEU 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 511 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 627 HIS Chi-restraints excluded: chain B residue 66 VAL 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 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128749 restraints weight = 8284.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130885 restraints weight = 5125.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131503 restraints weight = 3845.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131792 restraints weight = 3507.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132723 restraints weight = 3168.543| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2797 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= 0.170 Angle : 0.556 6.665 7601 Z= 0.294 Chirality : 0.043 0.365 881 Planarity : 0.004 0.043 991 Dihedral : 3.959 15.915 761 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.32), residues: 691 helix: 1.32 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.010 0.001 TYR A 440 PHE 0.022 0.002 PHE A 626 TRP 0.005 0.001 TRP A 209 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5605) covalent geometry : angle 0.55650 ( 7601) hydrogen bonds : bond 0.03247 ( 307) hydrogen bonds : angle 3.60945 ( 909) *********************** 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 98 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.216 Fit side-chains REVERT: A 105 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7304 (tptt) REVERT: A 139 TYR cc_start: 0.8164 (t80) cc_final: 0.7904 (t80) outliers start: 23 outliers final: 22 residues processed: 88 average time/residue: 0.0678 time to fit residues: 8.1824 Evaluate side-chains 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR 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 237 LEU 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 511 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 627 HIS Chi-restraints excluded: chain B residue 66 VAL 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 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 42 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 41 optimal weight: 0.0870 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132117 restraints weight = 8194.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134069 restraints weight = 5102.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135100 restraints weight = 3775.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135524 restraints weight = 3310.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135973 restraints weight = 2957.743| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5605 Z= 0.114 Angle : 0.533 7.566 7601 Z= 0.283 Chirality : 0.041 0.328 881 Planarity : 0.004 0.046 991 Dihedral : 3.882 18.497 761 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.53 % Allowed : 19.16 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.32), residues: 691 helix: 1.57 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.010 0.001 TYR A 69 PHE 0.019 0.002 PHE A 626 TRP 0.003 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5605) covalent geometry : angle 0.53303 ( 7601) hydrogen bonds : bond 0.03069 ( 307) hydrogen bonds : angle 3.43904 ( 909) *********************** 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 100 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.218 Fit side-chains REVERT: A 105 LYS cc_start: 0.7605 (mmmm) cc_final: 0.7295 (tptt) REVERT: A 121 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7754 (t0) REVERT: A 139 TYR cc_start: 0.8046 (t80) cc_final: 0.7724 (t80) REVERT: A 417 GLU cc_start: 0.7824 (tp30) cc_final: 0.7347 (tp30) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.0742 time to fit residues: 9.3983 Evaluate side-chains 90 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 237 LEU 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 511 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 582 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 627 HIS Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129134 restraints weight = 8343.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131467 restraints weight = 5329.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131947 restraints weight = 3985.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132568 restraints weight = 3586.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132619 restraints weight = 3177.775| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5605 Z= 0.151 Angle : 0.578 8.325 7601 Z= 0.303 Chirality : 0.043 0.415 881 Planarity : 0.004 0.052 991 Dihedral : 3.935 17.692 761 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.19 % Allowed : 19.66 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.32), residues: 691 helix: 1.46 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 33 TYR 0.009 0.001 TYR A 440 PHE 0.021 0.002 PHE A 626 TRP 0.006 0.001 TRP A 209 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5605) covalent geometry : angle 0.57826 ( 7601) hydrogen bonds : bond 0.03116 ( 307) hydrogen bonds : angle 3.51508 ( 909) ********************** 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 94 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.191 Fit side-chains REVERT: A 105 LYS cc_start: 0.7604 (mmmm) cc_final: 0.7304 (tptt) REVERT: A 139 TYR cc_start: 0.8090 (t80) cc_final: 0.7825 (t80) outliers start: 19 outliers final: 16 residues processed: 87 average time/residue: 0.0732 time to fit residues: 8.6173 Evaluate side-chains 87 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 237 LEU 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 511 ASN Chi-restraints excluded: chain A residue 551 THR 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 627 HIS Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130063 restraints weight = 8266.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132744 restraints weight = 5258.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133065 restraints weight = 3774.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133738 restraints weight = 3608.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133754 restraints weight = 3136.661| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2972 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= 0.131 Angle : 0.575 8.112 7601 Z= 0.302 Chirality : 0.043 0.407 881 Planarity : 0.004 0.041 991 Dihedral : 3.969 20.172 761 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.53 % Allowed : 19.50 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.32), residues: 691 helix: 1.52 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.76 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 33 TYR 0.010 0.001 TYR A 69 PHE 0.020 0.002 PHE A 626 TRP 0.006 0.001 TRP A 209 HIS 0.009 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5605) covalent geometry : angle 0.57492 ( 7601) hydrogen bonds : bond 0.03089 ( 307) hydrogen bonds : angle 3.48727 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.11 seconds wall clock time: 27 minutes 42.78 seconds (1662.78 seconds total)