Starting phenix.real_space_refine on Mon Jun 9 15:30:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpb_60331/06_2025/8zpb_60331_trim.cif" } resolution = 2.6 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= 0.024 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3560 2.51 5 N 845 2.21 5 O 986 1.98 5 H 5257 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10676 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 8801 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1779 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 93 Unusual residues: {' CL': 1, ' NA': 2, 'LNR': 1, 'PTY': 1} Classifications: {'undetermined': 5, 'water': 51} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 9.64, per 1000 atoms: 0.90 Number of scatterers: 10676 At special positions: 0 Unit cell: (98.44, 74.52, 79.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 24 16.00 P 1 15.00 Na 2 11.00 O 986 8.00 N 845 7.00 C 3560 6.00 H 5257 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 788.3 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 69.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.631A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 121 removed outlier: 3.972A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 4.825A pdb=" N MET A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.771A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.207A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.804A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.631A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.205A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.820A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.688A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.580A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.555A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.399A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.037A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.912A pdb=" N ARG A 56 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.692A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 340 hydrogen bonds defined for protein. 951 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: 6.25 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5250 1.03 - 1.23: 20 1.23 - 1.42: 2447 1.42 - 1.62: 3026 1.62 - 1.81: 39 Bond restraints: 10782 Sorted by residual: bond pdb=" CAE LNR A 701 " pdb=" CAI LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" CAG LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CAF LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" CAI LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.402 1.317 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAG LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.395 1.316 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 10777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 18221 1.14 - 2.28: 1067 2.28 - 3.42: 70 3.42 - 4.57: 19 4.57 - 5.71: 3 Bond angle restraints: 19380 Sorted by residual: angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 112.75 108.87 3.88 1.36e+00 5.41e-01 8.15e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" O SER A 182 " ideal model delta sigma weight residual 121.01 117.76 3.25 1.18e+00 7.18e-01 7.61e+00 angle pdb=" N PRO A 183 " pdb=" CA PRO A 183 " pdb=" C PRO A 183 " ideal model delta sigma weight residual 114.35 110.97 3.38 1.25e+00 6.40e-01 7.31e+00 angle pdb=" CA TRP A 80 " pdb=" C TRP A 80 " pdb=" O TRP A 80 " ideal model delta sigma weight residual 119.41 116.41 3.00 1.13e+00 7.83e-01 7.07e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 117.60 120.69 -3.09 1.18e+00 7.18e-01 6.85e+00 ... (remaining 19375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 4766 23.82 - 47.64: 267 47.64 - 71.46: 85 71.46 - 95.28: 2 95.28 - 119.11: 1 Dihedral angle restraints: 5121 sinusoidal: 2620 harmonic: 2501 Sorted by residual: dihedral pdb=" N1 PTY A 705 " pdb=" C2 PTY A 705 " pdb=" C3 PTY A 705 " pdb=" O11 PTY A 705 " ideal model delta sinusoidal sigma weight residual 65.33 -175.56 -119.11 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" N GLN B 52 " pdb=" CA GLN B 52 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 128 " pdb=" C TRP A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 665 0.046 - 0.091: 129 0.091 - 0.137: 30 0.137 - 0.182: 1 0.182 - 0.228: 1 Chirality restraints: 826 Sorted by residual: chirality pdb=" CAL LNR A 701 " pdb=" CAH LNR A 701 " pdb=" CAK LNR A 701 " pdb=" OAD LNR A 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 79 " pdb=" N VAL A 79 " pdb=" C VAL A 79 " pdb=" CB VAL A 79 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL B 2 " pdb=" N VAL B 2 " pdb=" C VAL B 2 " pdb=" CB VAL B 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 823 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LEU A 102 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 102 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 213 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE A 213 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 213 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 214 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 392 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.020 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 629 2.19 - 2.79: 21815 2.79 - 3.39: 32592 3.39 - 4.00: 43958 4.00 - 4.60: 68263 Nonbonded interactions: 167257 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb="HH22 ARG B 71 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU B 6 " pdb=" H CYS B 95 " model vdw 1.602 2.450 nonbonded pdb=" O PHE A 495 " pdb="HE21 GLN A 608 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU B 6 " pdb=" H GLY B 113 " model vdw 1.655 2.450 nonbonded pdb="HH22 ARG A 81 " pdb=" O HOH A 810 " model vdw 1.663 2.450 ... (remaining 167252 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 individual isotropic 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: 9.550 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: 0.200 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.560 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:29.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 5527 Z= 0.261 Angle : 0.563 5.707 7530 Z= 0.328 Chirality : 0.039 0.228 826 Planarity : 0.004 0.051 922 Dihedral : 15.800 119.105 1882 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.08 % Allowed : 14.52 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.33), residues: 659 helix: 1.10 (0.27), residues: 389 sheet: -1.46 (0.86), residues: 33 loop : 0.24 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 PHE 0.014 0.001 PHE A 409 TYR 0.015 0.002 TYR A 572 ARG 0.009 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.12741 ( 334) hydrogen bonds : angle 6.00121 ( 951) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.68477 ( 4) covalent geometry : bond 0.00512 ( 5525) covalent geometry : angle 0.56311 ( 7526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7750 (t60) REVERT: A 121 ARG cc_start: 0.8502 (mtm180) cc_final: 0.7511 (mtp180) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 2.0000 time to fit residues: 190.8750 Evaluate side-chains 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126381 restraints weight = 14931.861| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.08 r_work: 0.3583 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5527 Z= 0.161 Angle : 0.510 5.589 7530 Z= 0.277 Chirality : 0.038 0.130 826 Planarity : 0.005 0.058 922 Dihedral : 8.143 70.756 757 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 13.26 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.33), residues: 659 helix: 1.25 (0.27), residues: 385 sheet: -1.77 (0.71), residues: 33 loop : 0.70 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 556 HIS 0.003 0.001 HIS A 613 PHE 0.015 0.001 PHE A 409 TYR 0.014 0.002 TYR A 87 ARG 0.005 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 334) hydrogen bonds : angle 5.17974 ( 951) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.96740 ( 4) covalent geometry : bond 0.00355 ( 5525) covalent geometry : angle 0.51002 ( 7526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7639 (t60) REVERT: A 121 ARG cc_start: 0.8402 (mtm180) cc_final: 0.7542 (mtp180) REVERT: A 206 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6780 (tttt) REVERT: A 341 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7234 (ptm-80) REVERT: A 509 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7777 (mtm) REVERT: A 612 GLN cc_start: 0.7744 (mp-120) cc_final: 0.7511 (pm20) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.8926 time to fit residues: 182.9432 Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117149 restraints weight = 15208.959| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.08 r_work: 0.3581 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5527 Z= 0.159 Angle : 0.499 5.481 7530 Z= 0.270 Chirality : 0.038 0.129 826 Planarity : 0.004 0.048 922 Dihedral : 7.463 68.903 755 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.33 % Allowed : 12.54 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.33), residues: 659 helix: 1.22 (0.27), residues: 389 sheet: -1.80 (0.68), residues: 33 loop : 0.86 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE A 316 TYR 0.014 0.002 TYR A 87 ARG 0.005 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 334) hydrogen bonds : angle 5.08992 ( 951) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.94115 ( 4) covalent geometry : bond 0.00353 ( 5525) covalent geometry : angle 0.49834 ( 7526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7746 (t60) REVERT: A 121 ARG cc_start: 0.8398 (mtm180) cc_final: 0.7574 (mtp180) REVERT: A 206 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6785 (tttt) REVERT: A 341 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7229 (ptm-80) REVERT: A 509 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7678 (mtm) REVERT: B 56 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8208 (ttp80) REVERT: B 115 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7535 (tm-30) outliers start: 13 outliers final: 5 residues processed: 90 average time/residue: 2.0452 time to fit residues: 195.0526 Evaluate side-chains 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125899 restraints weight = 13887.312| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.94 r_work: 0.3154 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5527 Z= 0.132 Angle : 0.474 5.359 7530 Z= 0.256 Chirality : 0.037 0.125 826 Planarity : 0.004 0.042 922 Dihedral : 6.914 67.261 755 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.97 % Allowed : 12.90 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.34), residues: 659 helix: 1.42 (0.27), residues: 385 sheet: -1.46 (0.70), residues: 33 loop : 0.82 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.001 PHE A 316 TYR 0.013 0.001 TYR A 87 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 334) hydrogen bonds : angle 4.90482 ( 951) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.77764 ( 4) covalent geometry : bond 0.00289 ( 5525) covalent geometry : angle 0.47340 ( 7526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7678 (t60) REVERT: A 121 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7267 (mtp180) REVERT: A 304 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: A 359 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: B 115 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7201 (tm-30) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 1.9729 time to fit residues: 190.4637 Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124120 restraints weight = 14001.890| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.94 r_work: 0.3110 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5527 Z= 0.151 Angle : 0.486 5.304 7530 Z= 0.263 Chirality : 0.037 0.125 826 Planarity : 0.004 0.044 922 Dihedral : 6.311 61.806 752 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.79 % Allowed : 13.62 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.34), residues: 659 helix: 1.40 (0.27), residues: 385 sheet: -1.63 (0.69), residues: 39 loop : 0.96 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 59 HIS 0.002 0.001 HIS A 220 PHE 0.014 0.001 PHE A 409 TYR 0.013 0.001 TYR A 87 ARG 0.007 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 334) hydrogen bonds : angle 4.95553 ( 951) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.93229 ( 4) covalent geometry : bond 0.00338 ( 5525) covalent geometry : angle 0.48537 ( 7526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8417 (OUTLIER) cc_final: 0.7700 (t60) REVERT: A 121 ARG cc_start: 0.8284 (mtm180) cc_final: 0.7227 (mtp180) REVERT: A 304 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: A 341 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7184 (ptm-80) REVERT: A 359 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 56 ARG cc_start: 0.8496 (tmm-80) cc_final: 0.8099 (ttp80) REVERT: B 115 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7178 (tm-30) outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 2.0665 time to fit residues: 194.3485 Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125409 restraints weight = 13992.798| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.94 r_work: 0.3146 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5527 Z= 0.134 Angle : 0.473 5.244 7530 Z= 0.255 Chirality : 0.037 0.124 826 Planarity : 0.004 0.042 922 Dihedral : 6.150 62.318 752 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 14.16 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.34), residues: 659 helix: 1.49 (0.27), residues: 385 sheet: -1.56 (0.70), residues: 39 loop : 0.98 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.001 PHE A 316 TYR 0.012 0.001 TYR B 30 ARG 0.007 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 334) hydrogen bonds : angle 4.86947 ( 951) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.78132 ( 4) covalent geometry : bond 0.00297 ( 5525) covalent geometry : angle 0.47232 ( 7526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7682 (t60) REVERT: A 121 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7239 (mtp180) REVERT: A 304 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: B 115 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7241 (tm-30) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 2.0287 time to fit residues: 193.8915 Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.109396 restraints weight = 14923.501| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.20 r_work: 0.3049 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5527 Z= 0.154 Angle : 0.486 5.235 7530 Z= 0.263 Chirality : 0.037 0.126 826 Planarity : 0.004 0.044 922 Dihedral : 6.245 64.911 752 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 14.16 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.34), residues: 659 helix: 1.43 (0.27), residues: 385 sheet: -1.57 (0.70), residues: 39 loop : 0.97 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 59 HIS 0.002 0.001 HIS A 220 PHE 0.014 0.001 PHE A 409 TYR 0.013 0.001 TYR A 87 ARG 0.006 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 334) hydrogen bonds : angle 4.93753 ( 951) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.95794 ( 4) covalent geometry : bond 0.00344 ( 5525) covalent geometry : angle 0.48557 ( 7526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.7680 (t60) REVERT: A 121 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7122 (mtp180) REVERT: A 304 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: A 359 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 56 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8134 (ttp80) REVERT: B 115 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7162 (tm-30) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 2.1503 time to fit residues: 197.9422 Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126778 restraints weight = 13942.535| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.94 r_work: 0.3134 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5527 Z= 0.143 Angle : 0.477 5.211 7530 Z= 0.258 Chirality : 0.037 0.124 826 Planarity : 0.004 0.043 922 Dihedral : 6.175 65.062 752 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.79 % Allowed : 13.98 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 659 helix: 1.48 (0.27), residues: 385 sheet: -1.57 (0.70), residues: 39 loop : 0.97 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.001 PHE A 316 TYR 0.014 0.001 TYR B 30 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 334) hydrogen bonds : angle 4.88947 ( 951) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.83265 ( 4) covalent geometry : bond 0.00317 ( 5525) covalent geometry : angle 0.47629 ( 7526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8415 (OUTLIER) cc_final: 0.7684 (t60) REVERT: A 121 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7239 (mtp180) REVERT: A 304 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: A 359 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 509 MET cc_start: 0.8090 (mtm) cc_final: 0.7475 (mtt) REVERT: B 56 ARG cc_start: 0.8450 (tmm-80) cc_final: 0.8152 (ttp80) REVERT: B 115 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7245 (tm-30) outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 2.0199 time to fit residues: 188.1172 Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109782 restraints weight = 14806.586| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.18 r_work: 0.3029 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5527 Z= 0.146 Angle : 0.481 5.205 7530 Z= 0.260 Chirality : 0.037 0.126 826 Planarity : 0.004 0.043 922 Dihedral : 6.164 65.436 752 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.43 % Allowed : 14.16 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 659 helix: 1.47 (0.27), residues: 385 sheet: -1.59 (0.70), residues: 39 loop : 0.97 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 PHE 0.014 0.001 PHE A 409 TYR 0.014 0.001 TYR A 87 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 334) hydrogen bonds : angle 4.90103 ( 951) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.86294 ( 4) covalent geometry : bond 0.00325 ( 5525) covalent geometry : angle 0.48056 ( 7526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7679 (t60) REVERT: A 121 ARG cc_start: 0.8303 (mtm180) cc_final: 0.7225 (mtp180) REVERT: A 304 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: A 359 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 31 GLN cc_start: 0.8303 (mt0) cc_final: 0.8049 (mt0) REVERT: B 56 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.8173 (ttp80) REVERT: B 115 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7178 (tm-30) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 2.0312 time to fit residues: 186.9790 Evaluate side-chains 89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112212 restraints weight = 14733.878| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.12 r_work: 0.3065 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5527 Z= 0.132 Angle : 0.471 5.179 7530 Z= 0.254 Chirality : 0.037 0.125 826 Planarity : 0.004 0.043 922 Dihedral : 6.065 64.889 752 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 13.98 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.34), residues: 659 helix: 1.53 (0.27), residues: 385 sheet: -1.54 (0.71), residues: 39 loop : 1.00 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 PHE 0.012 0.001 PHE A 316 TYR 0.015 0.001 TYR B 30 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 334) hydrogen bonds : angle 4.83371 ( 951) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.74627 ( 4) covalent geometry : bond 0.00292 ( 5525) covalent geometry : angle 0.47062 ( 7526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7668 (t60) REVERT: A 121 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7176 (mtp180) REVERT: A 304 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: A 359 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 509 MET cc_start: 0.8102 (mtm) cc_final: 0.7483 (mtt) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 2.1393 time to fit residues: 190.0447 Evaluate side-chains 87 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.126718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108272 restraints weight = 14796.908| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.16 r_work: 0.3009 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5527 Z= 0.184 Angle : 0.511 5.228 7530 Z= 0.277 Chirality : 0.038 0.128 826 Planarity : 0.004 0.046 922 Dihedral : 6.354 67.419 752 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 13.98 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.34), residues: 659 helix: 1.36 (0.27), residues: 385 sheet: -1.63 (0.70), residues: 39 loop : 0.95 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 PHE 0.016 0.001 PHE A 409 TYR 0.016 0.002 TYR A 87 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 334) hydrogen bonds : angle 5.05469 ( 951) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.09552 ( 4) covalent geometry : bond 0.00419 ( 5525) covalent geometry : angle 0.51094 ( 7526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8661.30 seconds wall clock time: 151 minutes 38.83 seconds (9098.83 seconds total)