Starting phenix.real_space_refine on Thu Jul 2 01:01:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_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 { model { file = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9p_31035/07_2026/7e9p_31035.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 chiralities: 1 Time building chain proxies: 0.91, per 1000 atoms: 0.19 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: 0.26 Conformation dependent library (CDL) restraints added in 110.0 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: 0.13 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: 0.60 Time building geometry restraints manager: 0.37 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 - 17.07: 2641 17.07 - 34.14: 274 34.14 - 51.21: 44 51.21 - 68.27: 9 68.27 - 85.34: 3 Dihedral angle restraints: 2971 sinusoidal: 1133 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 2968 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: 2.800 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 5026 Z= 0.279 Angle : 0.795 9.461 6846 Z= 0.458 Chirality : 0.048 0.262 755 Planarity : 0.004 0.038 885 Dihedral : 13.866 85.342 1780 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG B 408 TYR 0.034 0.002 TYR B 473 PHE 0.020 0.001 PHE H 139 TRP 0.015 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.28 ( 5018) covalent geometry : angle 0.78342 / 0.46 ( 6829) SS BOND : bond 0.00633 / 0.28 ( 7) SS BOND : angle 1.08115 / 0.65 ( 14) hydrogen bonds : bond 0.13273 / 7.00 ( 162) hydrogen bonds : angle 6.75560 / 4.57 ( 387) link_NAG-ASN : bond 0.01099 / 0.58 ( 1) link_NAG-ASN : angle 6.35897 / 2.98 ( 3) *********************** 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 : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8922 (mp) cc_final: 0.8706 (mt) REVERT: H 30 ASP cc_start: 0.7983 (p0) cc_final: 0.7572 (p0) REVERT: H 31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7576 (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: 0.0599 time to fit residues: 5.5357 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.104806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090569 restraints weight = 11299.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092835 restraints weight = 5661.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094297 restraints weight = 3428.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095170 restraints weight = 2347.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095845 restraints weight = 1796.005| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5026 Z= 0.135 Angle : 0.633 10.260 6846 Z= 0.321 Chirality : 0.045 0.269 755 Planarity : 0.004 0.038 885 Dihedral : 4.740 19.016 692 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.37 % Allowed : 9.80 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.32), residues: 629 helix: -3.55 (0.73), residues: 25 sheet: -0.43 (0.33), residues: 244 loop : -2.10 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.020 0.001 TYR B 453 PHE 0.013 0.001 PHE H 139 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5018) covalent geometry : angle 0.62462 / 0.32 ( 6829) SS BOND : bond 0.00637 / 0.26 ( 7) SS BOND : angle 1.05737 / 0.65 ( 14) hydrogen bonds : bond 0.03335 / 1.97 ( 162) hydrogen bonds : angle 5.94121 / 3.90 ( 387) link_NAG-ASN : bond 0.00994 / 0.52 ( 1) link_NAG-ASN : angle 4.57896 / 2.15 ( 3) *********************** 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 69 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8971 (mp) cc_final: 0.8761 (mt) REVERT: H 30 ASP cc_start: 0.8175 (p0) cc_final: 0.7883 (p0) REVERT: H 31 ASP cc_start: 0.8097 (m-30) cc_final: 0.7624 (m-30) REVERT: H 161 ASP cc_start: 0.8219 (m-30) cc_final: 0.7969 (m-30) outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.0539 time to fit residues: 5.0895 Evaluate side-chains 52 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094350 restraints weight = 11207.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096667 restraints weight = 5544.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098138 restraints weight = 3313.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099079 restraints weight = 2260.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099662 restraints weight = 1702.281| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5026 Z= 0.129 Angle : 0.593 6.581 6846 Z= 0.304 Chirality : 0.045 0.248 755 Planarity : 0.004 0.034 885 Dihedral : 4.489 18.976 692 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.48 % Allowed : 12.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.32), residues: 629 helix: -3.87 (0.74), residues: 18 sheet: -0.26 (0.34), residues: 244 loop : -2.09 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 59 TYR 0.027 0.001 TYR B 473 PHE 0.011 0.001 PHE B 456 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5018) covalent geometry : angle 0.58796 / 0.30 ( 6829) SS BOND : bond 0.00650 / 0.26 ( 7) SS BOND : angle 0.86599 / 0.53 ( 14) hydrogen bonds : bond 0.03210 / 1.91 ( 162) hydrogen bonds : angle 5.73500 / 3.76 ( 387) link_NAG-ASN : bond 0.00644 / 0.34 ( 1) link_NAG-ASN : angle 3.35066 / 1.56 ( 3) *********************** 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 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9034 (mp) cc_final: 0.8809 (mt) REVERT: H 30 ASP cc_start: 0.8177 (p0) cc_final: 0.7821 (p0) REVERT: H 31 ASP cc_start: 0.8068 (m-30) cc_final: 0.7614 (m-30) REVERT: H 161 ASP cc_start: 0.8139 (m-30) cc_final: 0.7904 (m-30) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.0626 time to fit residues: 5.9254 Evaluate side-chains 60 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.109694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095299 restraints weight = 11024.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097514 restraints weight = 5585.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098946 restraints weight = 3402.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099786 restraints weight = 2341.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100433 restraints weight = 1811.959| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5026 Z= 0.116 Angle : 0.633 10.452 6846 Z= 0.322 Chirality : 0.045 0.266 755 Planarity : 0.004 0.034 885 Dihedral : 4.351 16.714 692 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.66 % Allowed : 14.79 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.32), residues: 629 helix: -4.13 (0.65), residues: 18 sheet: -0.19 (0.34), residues: 241 loop : -1.99 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.018 0.001 TYR B 473 PHE 0.015 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5018) covalent geometry : angle 0.61610 / 0.32 ( 6829) SS BOND : bond 0.00585 / 0.24 ( 7) SS BOND : angle 3.03882 / 1.66 ( 14) hydrogen bonds : bond 0.03022 / 1.80 ( 162) hydrogen bonds : angle 5.57063 / 3.66 ( 387) link_NAG-ASN : bond 0.00589 / 0.31 ( 1) link_NAG-ASN : angle 2.78014 / 1.30 ( 3) *********************** 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 71 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9052 (mp) cc_final: 0.8816 (mt) REVERT: L 150 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7126 (tptp) REVERT: H 30 ASP cc_start: 0.8098 (p0) cc_final: 0.7739 (p0) REVERT: H 31 ASP cc_start: 0.8050 (m-30) cc_final: 0.7643 (m-30) REVERT: H 161 ASP cc_start: 0.8129 (m-30) cc_final: 0.7904 (m-30) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.0612 time to fit residues: 5.7352 Evaluate side-chains 62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 433 VAL 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 1 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3678 r_free = 0.3678 target = 0.107056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092217 restraints weight = 11498.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094495 restraints weight = 5658.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095939 restraints weight = 3388.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096885 restraints weight = 2317.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097461 restraints weight = 1756.136| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5026 Z= 0.184 Angle : 0.670 8.140 6846 Z= 0.344 Chirality : 0.046 0.234 755 Planarity : 0.004 0.037 885 Dihedral : 4.654 19.813 692 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.85 % Allowed : 15.71 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.32), residues: 629 helix: -4.42 (0.47), residues: 18 sheet: -0.15 (0.34), residues: 241 loop : -1.99 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 216 TYR 0.020 0.002 TYR B 453 PHE 0.013 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 5018) covalent geometry : angle 0.65795 / 0.34 ( 6829) SS BOND : bond 0.00520 / 0.23 ( 7) SS BOND : angle 2.55617 / 1.42 ( 14) hydrogen bonds : bond 0.03613 / 2.18 ( 162) hydrogen bonds : angle 5.73255 / 3.74 ( 387) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 2.64365 / 1.24 ( 3) *********************** 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 69 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9054 (mp) cc_final: 0.8832 (mt) REVERT: L 150 LYS cc_start: 0.7906 (tmtt) cc_final: 0.7371 (tptt) REVERT: H 30 ASP cc_start: 0.8151 (p0) cc_final: 0.7798 (p0) REVERT: H 31 ASP cc_start: 0.8144 (m-30) cc_final: 0.7725 (m-30) REVERT: H 161 ASP cc_start: 0.8060 (m-30) cc_final: 0.7831 (m-30) REVERT: H 221 ASN cc_start: 0.7159 (p0) cc_final: 0.6793 (p0) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.0703 time to fit residues: 6.2604 Evaluate side-chains 61 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 433 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093642 restraints weight = 11457.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095951 restraints weight = 5624.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097400 restraints weight = 3364.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098298 restraints weight = 2306.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098930 restraints weight = 1774.325| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5026 Z= 0.140 Angle : 0.647 9.591 6846 Z= 0.328 Chirality : 0.045 0.219 755 Planarity : 0.004 0.037 885 Dihedral : 4.488 18.650 692 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.03 % Allowed : 17.19 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.32), residues: 629 helix: -4.39 (0.50), residues: 18 sheet: -0.10 (0.34), residues: 241 loop : -1.95 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 216 TYR 0.014 0.001 TYR B 453 PHE 0.011 0.001 PHE B 392 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 5018) covalent geometry : angle 0.63389 / 0.32 ( 6829) SS BOND : bond 0.00462 / 0.21 ( 7) SS BOND : angle 2.70586 / 1.47 ( 14) hydrogen bonds : bond 0.03251 / 1.97 ( 162) hydrogen bonds : angle 5.60575 / 3.66 ( 387) link_NAG-ASN : bond 0.00411 / 0.22 ( 1) link_NAG-ASN : angle 2.39234 / 1.12 ( 3) *********************** 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 67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9046 (mp) cc_final: 0.8829 (mt) REVERT: L 148 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7223 (tm-30) REVERT: L 150 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7298 (tptt) REVERT: H 30 ASP cc_start: 0.8126 (p0) cc_final: 0.7786 (p0) REVERT: H 31 ASP cc_start: 0.8134 (m-30) cc_final: 0.7730 (m-30) REVERT: H 161 ASP cc_start: 0.8093 (m-30) cc_final: 0.7869 (m-30) REVERT: H 221 ASN cc_start: 0.7010 (p0) cc_final: 0.6649 (p0) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.0599 time to fit residues: 5.1595 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 : 0.125 ------------------------------------------------------------------------------- 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 433 VAL 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 187 LEU 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 37 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095131 restraints weight = 11201.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097441 restraints weight = 5549.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098933 restraints weight = 3340.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099881 restraints weight = 2286.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100501 restraints weight = 1724.241| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5026 Z= 0.110 Angle : 0.605 8.064 6846 Z= 0.308 Chirality : 0.043 0.206 755 Planarity : 0.004 0.037 885 Dihedral : 4.208 16.577 692 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.03 % Allowed : 17.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.33), residues: 629 helix: -4.21 (0.65), residues: 18 sheet: 0.06 (0.35), residues: 240 loop : -1.83 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 216 TYR 0.012 0.001 TYR B 473 PHE 0.013 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5018) covalent geometry : angle 0.59453 / 0.30 ( 6829) SS BOND : bond 0.00365 / 0.17 ( 7) SS BOND : angle 2.33157 / 1.27 ( 14) hydrogen bonds : bond 0.02913 / 1.74 ( 162) hydrogen bonds : angle 5.41689 / 3.55 ( 387) link_NAG-ASN : bond 0.00497 / 0.26 ( 1) link_NAG-ASN : angle 2.15898 / 1.01 ( 3) *********************** 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 72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9048 (mp) cc_final: 0.8813 (mt) REVERT: B 506 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: L 86 GLU cc_start: 0.7712 (tp30) cc_final: 0.7446 (tp30) REVERT: L 150 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7234 (tptt) REVERT: L 167 SER cc_start: 0.9060 (t) cc_final: 0.8854 (m) REVERT: L 200 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7225 (mm-30) REVERT: H 30 ASP cc_start: 0.8109 (p0) cc_final: 0.7799 (p0) REVERT: H 31 ASP cc_start: 0.8090 (m-30) cc_final: 0.7623 (m-30) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.0499 time to fit residues: 4.7076 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 : 0.170 ------------------------------------------------------------------------------- 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 187 LEU 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 5 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092984 restraints weight = 11297.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095264 restraints weight = 5531.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096735 restraints weight = 3318.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097671 restraints weight = 2265.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098315 restraints weight = 1715.092| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5026 Z= 0.159 Angle : 0.646 8.144 6846 Z= 0.333 Chirality : 0.044 0.217 755 Planarity : 0.004 0.039 885 Dihedral : 4.460 17.480 692 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.03 % Allowed : 17.74 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.33), residues: 629 helix: -3.92 (0.70), residues: 25 sheet: 0.11 (0.35), residues: 241 loop : -1.79 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 216 TYR 0.017 0.001 TYR B 453 PHE 0.012 0.001 PHE L 144 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5018) covalent geometry : angle 0.63691 / 0.33 ( 6829) SS BOND : bond 0.00452 / 0.21 ( 7) SS BOND : angle 2.30901 / 1.27 ( 14) hydrogen bonds : bond 0.03438 / 2.06 ( 162) hydrogen bonds : angle 5.57159 / 3.65 ( 387) link_NAG-ASN : bond 0.00310 / 0.16 ( 1) link_NAG-ASN : angle 2.17055 / 1.02 ( 3) *********************** 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 67 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9056 (mp) cc_final: 0.8838 (mt) REVERT: L 86 GLU cc_start: 0.7871 (tp30) cc_final: 0.7557 (tp30) REVERT: L 150 LYS cc_start: 0.7858 (tmtt) cc_final: 0.7266 (tptt) REVERT: H 30 ASP cc_start: 0.8121 (p0) cc_final: 0.7830 (p0) REVERT: H 31 ASP cc_start: 0.8129 (m-30) cc_final: 0.7651 (m-30) REVERT: H 161 ASP cc_start: 0.7836 (m-30) cc_final: 0.7567 (m-30) REVERT: H 221 ASN cc_start: 0.7101 (p0) cc_final: 0.6707 (p0) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.0519 time to fit residues: 4.7084 Evaluate side-chains 62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 433 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3726 r_free = 0.3726 target = 0.109735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094943 restraints weight = 11211.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097250 restraints weight = 5585.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098731 restraints weight = 3354.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099711 restraints weight = 2301.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100261 restraints weight = 1731.279| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5026 Z= 0.117 Angle : 0.624 8.607 6846 Z= 0.318 Chirality : 0.044 0.204 755 Planarity : 0.004 0.036 885 Dihedral : 4.248 16.915 692 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.29 % Allowed : 18.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.33), residues: 629 helix: -4.18 (0.71), residues: 18 sheet: 0.14 (0.35), residues: 240 loop : -1.84 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 216 TYR 0.011 0.001 TYR B 473 PHE 0.012 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5018) covalent geometry : angle 0.61410 / 0.31 ( 6829) SS BOND : bond 0.00366 / 0.17 ( 7) SS BOND : angle 2.33239 / 1.22 ( 14) hydrogen bonds : bond 0.02988 / 1.80 ( 162) hydrogen bonds : angle 5.39962 / 3.54 ( 387) link_NAG-ASN : bond 0.00430 / 0.23 ( 1) link_NAG-ASN : angle 2.07386 / 0.97 ( 3) *********************** 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: 7 poor density : 60 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9037 (mp) cc_final: 0.8808 (mt) REVERT: L 150 LYS cc_start: 0.7753 (tmtt) cc_final: 0.7217 (tptt) REVERT: L 167 SER cc_start: 0.9058 (t) cc_final: 0.8857 (m) REVERT: H 30 ASP cc_start: 0.8112 (p0) cc_final: 0.7807 (p0) REVERT: H 31 ASP cc_start: 0.8096 (m-30) cc_final: 0.7634 (m-30) REVERT: H 38 ARG cc_start: 0.8617 (ptm160) cc_final: 0.8395 (ttp80) REVERT: H 161 ASP cc_start: 0.7853 (m-30) cc_final: 0.7638 (m-30) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.0644 time to fit residues: 5.6728 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 : 0.195 ------------------------------------------------------------------------------- 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 187 LEU 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 35 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3719 r_free = 0.3719 target = 0.109286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094383 restraints weight = 11230.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096695 restraints weight = 5516.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098173 restraints weight = 3311.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099044 restraints weight = 2272.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099742 restraints weight = 1746.495| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5026 Z= 0.129 Angle : 0.640 9.874 6846 Z= 0.325 Chirality : 0.044 0.208 755 Planarity : 0.004 0.040 885 Dihedral : 4.283 17.478 692 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.66 % Allowed : 18.85 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.33), residues: 629 helix: -3.84 (0.74), residues: 25 sheet: 0.17 (0.35), residues: 242 loop : -1.72 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 216 TYR 0.012 0.001 TYR B 453 PHE 0.010 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5018) covalent geometry : angle 0.63126 / 0.32 ( 6829) SS BOND : bond 0.00417 / 0.19 ( 7) SS BOND : angle 2.25141 / 1.18 ( 14) hydrogen bonds : bond 0.03122 / 1.87 ( 162) hydrogen bonds : angle 5.40541 / 3.55 ( 387) link_NAG-ASN : bond 0.00395 / 0.21 ( 1) link_NAG-ASN : angle 2.06802 / 0.97 ( 3) ********************** 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 68 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.9053 (mp) cc_final: 0.8833 (mt) REVERT: L 150 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7247 (tptt) REVERT: L 167 SER cc_start: 0.9072 (t) cc_final: 0.8849 (m) REVERT: H 30 ASP cc_start: 0.8114 (p0) cc_final: 0.7807 (p0) REVERT: H 31 ASP cc_start: 0.8100 (m-30) cc_final: 0.7633 (m-30) REVERT: H 161 ASP cc_start: 0.7800 (m-30) cc_final: 0.7549 (m-30) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0623 time to fit residues: 5.7196 Evaluate side-chains 62 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain H residue 159 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 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 58 optimal weight: 2.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096721 restraints weight = 11149.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099144 restraints weight = 5469.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100706 restraints weight = 3263.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101670 restraints weight = 2211.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102182 restraints weight = 1670.509| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5026 Z= 0.106 Angle : 0.612 8.470 6846 Z= 0.311 Chirality : 0.043 0.195 755 Planarity : 0.004 0.037 885 Dihedral : 4.023 16.517 692 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.11 % Allowed : 20.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.33), residues: 629 helix: -4.08 (0.78), residues: 18 sheet: 0.21 (0.34), residues: 244 loop : -1.68 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 216 TYR 0.010 0.001 TYR B 473 PHE 0.013 0.001 PHE B 392 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5018) covalent geometry : angle 0.60612 / 0.31 ( 6829) SS BOND : bond 0.00341 / 0.16 ( 7) SS BOND : angle 1.84519 / 0.96 ( 14) hydrogen bonds : bond 0.02744 / 1.65 ( 162) hydrogen bonds : angle 5.21909 / 3.44 ( 387) link_NAG-ASN : bond 0.00500 / 0.26 ( 1) link_NAG-ASN : angle 1.93678 / 0.91 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 871.87 seconds wall clock time: 15 minutes 44.33 seconds (944.33 seconds total)