Starting phenix.real_space_refine on Tue Feb 11 09:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9p_31035/02_2025/7e9p_31035.cif" } resolution = 3.69 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= -0.004 sd= 0.036 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 22 5.16 5 C 3095 2.51 5 N 823 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.02, per 1000 atoms: 0.82 Number of scatterers: 4898 At special positions: 0 Unit cell: (70.08, 102.93, 98.55, 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 22 16.00 O 958 8.00 N 823 7.00 C 3095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 571.3 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 8.3% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.512A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.520A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.529A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.674A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.761A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.562A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.920A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.666A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 167 through 171 162 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 802 1.31 - 1.44: 1423 1.44 - 1.57: 2765 1.57 - 1.70: 0 1.70 - 1.83: 28 Bond restraints: 5018 Sorted by residual: bond pdb=" C7 NAG B1301 " pdb=" N2 NAG B1301 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" N GLU B 484 " pdb=" CA GLU B 484 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N LEU H 206 " pdb=" CA LEU H 206 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.27e-02 6.20e+03 1.26e+01 bond pdb=" N VAL B 483 " pdb=" CA VAL B 483 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 ... (remaining 5013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 6604 1.89 - 3.78: 189 3.78 - 5.68: 27 5.68 - 7.57: 6 7.57 - 9.46: 3 Bond angle restraints: 6829 Sorted by residual: angle pdb=" N PHE B 486 " pdb=" CA PHE B 486 " pdb=" C PHE B 486 " ideal model delta sigma weight residual 112.97 105.34 7.63 1.06e+00 8.90e-01 5.18e+01 angle pdb=" CA VAL B 483 " pdb=" C VAL B 483 " pdb=" O VAL B 483 " ideal model delta sigma weight residual 121.63 114.88 6.75 9.90e-01 1.02e+00 4.66e+01 angle pdb=" C GLU B 484 " pdb=" CA GLU B 484 " pdb=" CB GLU B 484 " ideal model delta sigma weight residual 110.78 101.60 9.18 1.60e+00 3.91e-01 3.29e+01 angle pdb=" N GLU B 484 " pdb=" CA GLU B 484 " pdb=" C GLU B 484 " ideal model delta sigma weight residual 108.20 117.66 -9.46 1.71e+00 3.42e-01 3.06e+01 angle pdb=" CB GLN B 474 " pdb=" CG GLN B 474 " pdb=" CD GLN B 474 " ideal model delta sigma weight residual 112.60 105.42 7.18 1.70e+00 3.46e-01 1.78e+01 ... (remaining 6824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 2774 23.00 - 46.00: 184 46.00 - 69.00: 23 69.00 - 92.00: 3 92.00 - 115.00: 8 Dihedral angle restraints: 2992 sinusoidal: 1154 harmonic: 1838 Sorted by residual: dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 141.21 -48.21 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 48.54 44.46 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 583 0.052 - 0.105: 144 0.105 - 0.157: 23 0.157 - 0.210: 4 0.210 - 0.262: 1 Chirality restraints: 755 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LEU H 206 " pdb=" N LEU H 206 " pdb=" C LEU H 206 " pdb=" CB LEU H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA PHE B 486 " pdb=" N PHE B 486 " pdb=" C PHE B 486 " pdb=" CB PHE B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 752 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 473 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.96e+00 pdb=" CG TYR B 473 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 473 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 473 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 473 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 473 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 473 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.015 2.00e-02 2.50e+03 1.15e-02 2.65e+00 pdb=" CG TYR B 453 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 473 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C TYR B 473 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR B 473 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN B 474 " -0.009 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 690 2.75 - 3.29: 4535 3.29 - 3.83: 7332 3.83 - 4.36: 8186 4.36 - 4.90: 15089 Nonbonded interactions: 35832 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.221 3.040 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.260 3.120 nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.278 3.040 nonbonded pdb=" O ARG L 147 " pdb=" NH1 ARG L 147 " model vdw 2.304 3.120 ... (remaining 35827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.108 5018 Z= 0.347 Angle : 0.783 9.461 6829 Z= 0.456 Chirality : 0.048 0.262 755 Planarity : 0.004 0.038 885 Dihedral : 16.126 115.002 1801 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 629 helix: -3.97 (0.66), residues: 25 sheet: -0.64 (0.33), residues: 240 loop : -2.30 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.001 PHE H 139 TYR 0.034 0.002 TYR B 473 ARG 0.005 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8922 (mp) cc_final: 0.8705 (mt) REVERT: H 30 ASP cc_start: 0.7983 (p0) cc_final: 0.7570 (p0) REVERT: H 31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7574 (m-30) REVERT: H 161 ASP cc_start: 0.8187 (m-30) cc_final: 0.7939 (m-30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1733 time to fit residues: 15.8511 Evaluate side-chains 61 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN H 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084886 restraints weight = 11321.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087085 restraints weight = 5913.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088493 restraints weight = 3647.408| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5018 Z= 0.199 Angle : 0.639 10.478 6829 Z= 0.321 Chirality : 0.046 0.265 755 Planarity : 0.004 0.038 885 Dihedral : 7.410 53.357 713 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.37 % Allowed : 9.61 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.32), residues: 629 helix: -4.00 (0.66), residues: 25 sheet: -0.44 (0.33), residues: 244 loop : -2.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.001 PHE H 139 TYR 0.020 0.001 TYR B 453 ARG 0.003 0.000 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 148 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7139 (tm-30) REVERT: H 30 ASP cc_start: 0.8248 (p0) cc_final: 0.7973 (p0) REVERT: H 31 ASP cc_start: 0.8233 (m-30) cc_final: 0.7774 (m-30) REVERT: H 161 ASP cc_start: 0.8253 (m-30) cc_final: 0.7989 (m-30) REVERT: H 221 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7149 (p0) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.1554 time to fit residues: 14.1160 Evaluate side-chains 56 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain H residue 221 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.097440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083334 restraints weight = 11402.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085496 restraints weight = 5929.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086903 restraints weight = 3656.865| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5018 Z= 0.234 Angle : 0.623 6.914 6829 Z= 0.316 Chirality : 0.046 0.290 755 Planarity : 0.004 0.035 885 Dihedral : 5.464 31.893 713 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.66 % Allowed : 12.38 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.32), residues: 629 helix: -3.67 (0.66), residues: 31 sheet: -0.28 (0.34), residues: 242 loop : -2.07 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE B 456 TYR 0.027 0.002 TYR B 473 ARG 0.003 0.000 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8232 (p0) cc_final: 0.7960 (p0) REVERT: H 31 ASP cc_start: 0.8260 (m-30) cc_final: 0.7817 (m-30) REVERT: H 161 ASP cc_start: 0.8209 (m-30) cc_final: 0.7959 (m-30) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.1613 time to fit residues: 14.5912 Evaluate side-chains 58 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081006 restraints weight = 11843.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083150 restraints weight = 6140.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084596 restraints weight = 3809.647| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5018 Z= 0.333 Angle : 0.728 11.731 6829 Z= 0.370 Chirality : 0.049 0.316 755 Planarity : 0.004 0.038 885 Dihedral : 5.329 31.380 713 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.59 % Allowed : 15.34 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.32), residues: 629 helix: -3.88 (0.61), residues: 31 sheet: -0.30 (0.34), residues: 239 loop : -2.13 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE B 392 TYR 0.023 0.002 TYR B 453 ARG 0.004 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: L 150 LYS cc_start: 0.7808 (tmtt) cc_final: 0.7266 (tptp) REVERT: H 30 ASP cc_start: 0.8232 (p0) cc_final: 0.7949 (p0) REVERT: H 161 ASP cc_start: 0.8103 (m-30) cc_final: 0.7856 (m-30) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.1743 time to fit residues: 15.6207 Evaluate side-chains 60 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089697 restraints weight = 11463.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091971 restraints weight = 5733.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093454 restraints weight = 3476.942| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5018 Z= 0.195 Angle : 0.622 8.878 6829 Z= 0.314 Chirality : 0.045 0.245 755 Planarity : 0.004 0.033 885 Dihedral : 4.725 26.486 713 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.03 % Allowed : 17.38 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.95 (0.32), residues: 629 helix: -3.56 (0.76), residues: 25 sheet: -0.16 (0.34), residues: 241 loop : -2.01 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE B 392 TYR 0.015 0.001 TYR B 473 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8110 (p0) cc_final: 0.7838 (p0) REVERT: H 161 ASP cc_start: 0.8175 (m-30) cc_final: 0.7950 (m-30) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1556 time to fit residues: 14.4844 Evaluate side-chains 63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087399 restraints weight = 11535.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089610 restraints weight = 5786.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091072 restraints weight = 3522.749| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5018 Z= 0.289 Angle : 0.692 11.200 6829 Z= 0.350 Chirality : 0.047 0.285 755 Planarity : 0.004 0.038 885 Dihedral : 5.068 30.156 713 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.03 % Allowed : 18.30 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.98 (0.32), residues: 629 helix: -3.63 (0.75), residues: 25 sheet: -0.15 (0.34), residues: 240 loop : -2.05 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE L 144 TYR 0.019 0.002 TYR B 453 ARG 0.003 0.000 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8093 (p0) cc_final: 0.7875 (p0) REVERT: H 161 ASP cc_start: 0.8103 (m-30) cc_final: 0.7878 (m-30) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.1925 time to fit residues: 16.3762 Evaluate side-chains 62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.3980 chunk 49 optimal weight: 0.0030 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.0060 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091625 restraints weight = 11372.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093977 restraints weight = 5757.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095377 restraints weight = 3482.560| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5018 Z= 0.161 Angle : 0.604 8.659 6829 Z= 0.306 Chirality : 0.043 0.221 755 Planarity : 0.004 0.032 885 Dihedral : 4.420 24.710 713 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.66 % Allowed : 18.67 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.32), residues: 629 helix: -4.16 (0.65), residues: 18 sheet: -0.02 (0.34), residues: 240 loop : -1.91 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.001 PHE B 392 TYR 0.012 0.001 TYR B 473 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: L 148 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7118 (tm-30) REVERT: L 150 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7206 (tptt) REVERT: H 30 ASP cc_start: 0.8100 (p0) cc_final: 0.7878 (p0) REVERT: H 38 ARG cc_start: 0.8600 (ptm160) cc_final: 0.8395 (ttp80) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.2092 time to fit residues: 19.0505 Evaluate side-chains 65 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.105903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091396 restraints weight = 11297.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093737 restraints weight = 5657.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095249 restraints weight = 3429.349| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5018 Z= 0.163 Angle : 0.595 7.213 6829 Z= 0.304 Chirality : 0.043 0.223 755 Planarity : 0.004 0.035 885 Dihedral : 4.308 24.296 713 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.48 % Allowed : 18.85 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.55 (0.33), residues: 629 helix: -4.13 (0.73), residues: 18 sheet: 0.18 (0.35), residues: 240 loop : -1.78 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.001 PHE B 392 TYR 0.011 0.001 TYR B 396 ARG 0.007 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8347 (mp10) REVERT: L 86 GLU cc_start: 0.7732 (tp30) cc_final: 0.7532 (tp30) REVERT: L 150 LYS cc_start: 0.7750 (tmtt) cc_final: 0.7230 (tptt) REVERT: L 167 SER cc_start: 0.9033 (t) cc_final: 0.8829 (m) REVERT: H 30 ASP cc_start: 0.8082 (p0) cc_final: 0.7868 (p0) REVERT: H 38 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8391 (ttp80) REVERT: H 161 ASP cc_start: 0.7889 (m-30) cc_final: 0.7618 (m-30) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.1813 time to fit residues: 16.7563 Evaluate side-chains 64 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.103482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089003 restraints weight = 11255.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091253 restraints weight = 5676.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.092708 restraints weight = 3438.072| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5018 Z= 0.246 Angle : 0.669 10.340 6829 Z= 0.337 Chirality : 0.045 0.265 755 Planarity : 0.004 0.040 885 Dihedral : 4.778 28.523 713 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.03 % Allowed : 18.85 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.68 (0.33), residues: 629 helix: -3.97 (0.68), residues: 25 sheet: 0.12 (0.35), residues: 239 loop : -1.84 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE L 144 TYR 0.016 0.001 TYR B 453 ARG 0.008 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: L 86 GLU cc_start: 0.7980 (tp30) cc_final: 0.7747 (tp30) REVERT: L 150 LYS cc_start: 0.7876 (tmtt) cc_final: 0.7320 (tptt) REVERT: H 30 ASP cc_start: 0.8141 (p0) cc_final: 0.7908 (p0) REVERT: H 161 ASP cc_start: 0.7886 (m-30) cc_final: 0.7571 (m-30) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1675 time to fit residues: 14.8531 Evaluate side-chains 63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** 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 = 0.3620 r_free = 0.3620 target = 0.104055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089655 restraints weight = 11430.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.091934 restraints weight = 5712.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093407 restraints weight = 3460.784| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5018 Z= 0.205 Angle : 0.648 10.495 6829 Z= 0.324 Chirality : 0.044 0.250 755 Planarity : 0.004 0.037 885 Dihedral : 4.638 27.355 713 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.03 % Allowed : 19.22 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.33), residues: 629 helix: -3.85 (0.74), residues: 25 sheet: 0.14 (0.34), residues: 241 loop : -1.80 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.010 0.001 PHE L 144 TYR 0.014 0.001 TYR B 453 ARG 0.008 0.000 ARG L 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: L 86 GLU cc_start: 0.7954 (tp30) cc_final: 0.7702 (tp30) REVERT: L 150 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7275 (tptt) REVERT: H 30 ASP cc_start: 0.8111 (p0) cc_final: 0.7891 (p0) REVERT: H 161 ASP cc_start: 0.7879 (m-30) cc_final: 0.7562 (m-30) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1511 time to fit residues: 13.1795 Evaluate side-chains 63 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.0070 chunk 58 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.106121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091449 restraints weight = 11296.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093834 restraints weight = 5619.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095373 restraints weight = 3385.235| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5018 Z= 0.161 Angle : 0.604 9.633 6829 Z= 0.302 Chirality : 0.043 0.221 755 Planarity : 0.004 0.036 885 Dihedral : 4.309 24.658 713 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.85 % Allowed : 19.04 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 629 helix: -4.14 (0.74), residues: 18 sheet: 0.16 (0.34), residues: 243 loop : -1.75 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.007 0.001 HIS H 35 PHE 0.012 0.001 PHE B 392 TYR 0.010 0.001 TYR B 396 ARG 0.007 0.000 ARG L 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.23 seconds wall clock time: 33 minutes 28.55 seconds (2008.55 seconds total)