Starting phenix.real_space_refine on Thu Mar 6 05:08:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9p_31035/03_2025/7e9p_31035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9p_31035/03_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_31035/03_2025/7e9p_31035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2025/7e9p_31035.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_2025/7e9p_31035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9p_31035/03_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-5624/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: 4.06, per 1000 atoms: 0.83 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: 1.16 Conformation dependent library (CDL) restraints added in 621.2 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: 1.41 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.840 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- 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 : 0.547 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: 0.1702 time to fit residues: 15.6207 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 : 0.548 ------------------------------------------------------------------------------- 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 = 0.098991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084859 restraints weight = 11322.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087050 restraints weight = 5952.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088483 restraints weight = 3674.772| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 10.477 6829 Z= 0.321 Chirality : 0.046 0.265 755 Planarity : 0.004 0.038 885 Dihedral : 7.411 53.364 713 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 : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 148 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7137 (tm-30) REVERT: H 30 ASP cc_start: 0.8247 (p0) cc_final: 0.7974 (p0) REVERT: H 31 ASP cc_start: 0.8233 (m-30) cc_final: 0.7774 (m-30) REVERT: H 161 ASP cc_start: 0.8256 (m-30) cc_final: 0.7991 (m-30) REVERT: H 221 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7152 (p0) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.1538 time to fit residues: 14.0188 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 : 0.508 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.097027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082934 restraints weight = 11433.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085079 restraints weight = 6019.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.086496 restraints weight = 3735.271| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5018 Z= 0.251 Angle : 0.632 7.260 6829 Z= 0.321 Chirality : 0.046 0.296 755 Planarity : 0.004 0.035 885 Dihedral : 5.465 32.125 713 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.85 % Allowed : 12.38 % Favored : 85.77 % 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: -2.12 (0.32), residues: 629 helix: -3.68 (0.66), residues: 31 sheet: -0.28 (0.34), residues: 242 loop : -2.08 (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 0.010 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 70 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8237 (p0) cc_final: 0.7962 (p0) REVERT: H 31 ASP cc_start: 0.8265 (m-30) cc_final: 0.7825 (m-30) REVERT: H 161 ASP cc_start: 0.8153 (m-30) cc_final: 0.7901 (m-30) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1577 time to fit residues: 14.4860 Evaluate side-chains 58 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080778 restraints weight = 11787.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082932 restraints weight = 6059.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084313 restraints weight = 3695.134| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5018 Z= 0.350 Angle : 0.712 11.255 6829 Z= 0.361 Chirality : 0.048 0.312 755 Planarity : 0.004 0.039 885 Dihedral : 5.410 31.950 713 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.59 % Allowed : 15.71 % Favored : 81.70 % 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: -3.93 (0.59), residues: 31 sheet: -0.29 (0.34), residues: 242 loop : -2.15 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.002 PHE L 144 TYR 0.025 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 72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 417 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (tptp) REVERT: B 470 THR cc_start: 0.8952 (p) cc_final: 0.8709 (p) REVERT: H 30 ASP cc_start: 0.8215 (p0) cc_final: 0.7916 (p0) REVERT: H 161 ASP cc_start: 0.8140 (m-30) cc_final: 0.7896 (m-30) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.1843 time to fit residues: 17.0159 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 : 0.549 ------------------------------------------------------------------------------- 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 417 LYS 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: 0.8980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.103753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089637 restraints weight = 11455.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091929 restraints weight = 5710.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093411 restraints weight = 3433.176| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5018 Z= 0.181 Angle : 0.610 9.697 6829 Z= 0.307 Chirality : 0.044 0.242 755 Planarity : 0.004 0.033 885 Dihedral : 4.681 26.272 713 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.48 % Allowed : 18.11 % Favored : 80.41 % 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: -1.94 (0.32), residues: 629 helix: -3.50 (0.78), residues: 25 sheet: -0.17 (0.34), residues: 241 loop : -1.99 (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 0.009 0.001 PHE B 456 TYR 0.016 0.001 TYR B 473 ARG 0.003 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 68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: L 148 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7198 (tm-30) REVERT: L 150 LYS cc_start: 0.7777 (tmtt) cc_final: 0.7220 (tptp) REVERT: H 30 ASP cc_start: 0.8107 (p0) cc_final: 0.7847 (p0) REVERT: H 161 ASP cc_start: 0.8160 (m-30) cc_final: 0.7940 (m-30) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.1899 time to fit residues: 17.3157 Evaluate side-chains 62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain H residue 64 VAL 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: 0.0970 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 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 = 0.105684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091222 restraints weight = 11321.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093563 restraints weight = 5639.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095068 restraints weight = 3410.860| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5018 Z= 0.161 Angle : 0.619 10.766 6829 Z= 0.313 Chirality : 0.044 0.241 755 Planarity : 0.004 0.035 885 Dihedral : 4.453 24.398 713 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.66 % Allowed : 18.30 % Favored : 80.04 % 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: -1.74 (0.32), residues: 629 helix: -3.45 (0.81), residues: 25 sheet: -0.01 (0.34), residues: 238 loop : -1.84 (0.30), residues: 366 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 0.013 0.001 TYR B 473 ARG 0.002 0.000 ARG H 87 *********************** 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 74 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: L 150 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7225 (tptt) REVERT: L 167 SER cc_start: 0.9048 (t) cc_final: 0.8835 (m) REVERT: H 30 ASP cc_start: 0.8097 (p0) cc_final: 0.7884 (p0) REVERT: H 38 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8399 (ttp80) REVERT: H 161 ASP cc_start: 0.8146 (m-30) cc_final: 0.7945 (m-30) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.2444 time to fit residues: 23.7133 Evaluate side-chains 65 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.102648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088378 restraints weight = 11376.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090621 restraints weight = 5714.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092074 restraints weight = 3466.953| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2285 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= 0.259 Angle : 0.677 10.111 6829 Z= 0.343 Chirality : 0.046 0.268 755 Planarity : 0.004 0.036 885 Dihedral : 4.857 28.687 713 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.66 % Allowed : 19.22 % 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: -1.78 (0.32), residues: 629 helix: -3.54 (0.78), residues: 25 sheet: -0.01 (0.34), residues: 239 loop : -1.91 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE L 144 TYR 0.018 0.002 TYR B 453 ARG 0.008 0.001 ARG L 216 *********************** 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 65 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: L 150 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7333 (tptt) REVERT: H 161 ASP cc_start: 0.8050 (m-30) cc_final: 0.7825 (m-30) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1616 time to fit residues: 13.8480 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 : 0.506 ------------------------------------------------------------------------------- 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 57 THR 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 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.0170 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.106193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091528 restraints weight = 11290.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093870 restraints weight = 5668.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095400 restraints weight = 3445.592| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2525 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 : 0.609 7.875 6829 Z= 0.309 Chirality : 0.043 0.217 755 Planarity : 0.004 0.036 885 Dihedral : 4.324 24.065 713 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.03 % Allowed : 19.41 % Favored : 78.56 % 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: -1.57 (0.33), residues: 629 helix: -4.07 (0.73), residues: 18 sheet: 0.16 (0.35), residues: 240 loop : -1.79 (0.30), residues: 371 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 0.014 0.001 PHE B 392 TYR 0.012 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 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: L 86 GLU cc_start: 0.7689 (tp30) cc_final: 0.7446 (tp30) REVERT: L 150 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7154 (tptt) REVERT: L 167 SER cc_start: 0.9046 (t) cc_final: 0.8845 (m) REVERT: H 38 ARG cc_start: 0.8596 (ptm160) cc_final: 0.8390 (ttp80) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1778 time to fit residues: 15.8782 Evaluate side-chains 66 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 127 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.104779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.090221 restraints weight = 11186.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092492 restraints weight = 5649.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093965 restraints weight = 3436.504| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5018 Z= 0.207 Angle : 0.628 8.131 6829 Z= 0.322 Chirality : 0.044 0.242 755 Planarity : 0.004 0.038 885 Dihedral : 4.494 26.414 713 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.03 % Allowed : 19.41 % Favored : 78.56 % 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: -1.64 (0.33), residues: 629 helix: -4.22 (0.65), residues: 18 sheet: 0.13 (0.35), residues: 241 loop : -1.86 (0.30), residues: 370 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 0.009 0.001 PHE B 456 TYR 0.013 0.001 TYR B 453 ARG 0.007 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 69 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: L 86 GLU cc_start: 0.7742 (tp30) cc_final: 0.7479 (tp30) REVERT: L 150 LYS cc_start: 0.7791 (tmtt) cc_final: 0.7241 (tptt) REVERT: H 161 ASP cc_start: 0.7872 (m-30) cc_final: 0.7558 (m-30) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1620 time to fit residues: 14.9993 Evaluate side-chains 64 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 127 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: 8.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.103264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088596 restraints weight = 11459.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090869 restraints weight = 5749.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092339 restraints weight = 3494.527| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5018 Z= 0.256 Angle : 0.674 10.116 6829 Z= 0.343 Chirality : 0.046 0.269 755 Planarity : 0.005 0.038 885 Dihedral : 4.791 29.027 713 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 19.96 % Favored : 78.00 % 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: -1.70 (0.32), residues: 629 helix: -4.37 (0.54), residues: 18 sheet: 0.12 (0.35), residues: 241 loop : -1.92 (0.29), residues: 370 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 0.017 0.001 TYR B 453 ARG 0.006 0.001 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 : 0.902 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: L 86 GLU cc_start: 0.7868 (tp30) cc_final: 0.7641 (tp30) REVERT: L 150 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7285 (tptt) REVERT: H 161 ASP cc_start: 0.7875 (m-30) cc_final: 0.7565 (m-30) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.2065 time to fit residues: 19.2032 Evaluate side-chains 64 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 127 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: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.102924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088299 restraints weight = 11432.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090542 restraints weight = 5793.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092017 restraints weight = 3541.860| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2550 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= 0.263 Angle : 0.689 10.305 6829 Z= 0.350 Chirality : 0.046 0.279 755 Planarity : 0.004 0.042 885 Dihedral : 4.953 29.582 713 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.22 % Allowed : 19.78 % Favored : 78.00 % 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: -1.75 (0.32), residues: 629 helix: -4.42 (0.50), residues: 18 sheet: 0.07 (0.34), residues: 243 loop : -1.94 (0.30), residues: 368 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 0.013 0.001 PHE L 144 TYR 0.017 0.001 TYR B 453 ARG 0.006 0.001 ARG L 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.33 seconds wall clock time: 38 minutes 14.22 seconds (2294.22 seconds total)