Starting phenix.real_space_refine on Thu Jul 2 01:54:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c44_16416/07_2026/8c44_16416.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 3363 2.51 5 N 896 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 5239 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3821 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 12, 'TRANS': 445} Chain breaks: 17 Chain: "C" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.19 Number of scatterers: 5239 At special positions: 0 Unit cell: (64.064, 74.048, 130.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 952 8.00 N 896 7.00 C 3363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.07 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1174 " distance=2.04 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 169 " distance=2.08 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 C 202 " - " ASN C 47 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 147.3 milliseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 62.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 571 through 594 Processing helix chain 'A' and resid 606 through 631 Processing helix chain 'A' and resid 646 through 660 removed outlier: 5.447A pdb=" N PHE A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 694 through 715 removed outlier: 3.572A pdb=" N ASN A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 869 through 892 Processing helix chain 'A' and resid 904 through 924 Processing helix chain 'A' and resid 931 through 950 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.611A pdb=" N MET A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.985A pdb=" N HIS A1005 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'A' and resid 1013 through 1035 Processing helix chain 'A' and resid 1069 through 1096 removed outlier: 3.743A pdb=" N GLN A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1125 Processing helix chain 'A' and resid 1161 through 1170 Processing helix chain 'C' and resid 58 through 87 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.502A pdb=" N TYR C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 828 removed outlier: 3.686A pdb=" N THR A 826 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.647A pdb=" N ALA C 31 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 40 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 29 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 42 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 27 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 25 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL C 112 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 127 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 114 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 125 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 116 " --> pdb=" O PHE C 123 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 948 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: 0.53 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1093 1.32 - 1.46: 1702 1.46 - 1.59: 2499 1.59 - 1.72: 24 1.72 - 1.85: 34 Bond restraints: 5352 Sorted by residual: bond pdb=" C THR A1154 " pdb=" N PRO A1155 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.31e-02 5.83e+03 2.50e+01 bond pdb=" N VAL C 124 " pdb=" CA VAL C 124 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.07e-02 8.73e+03 2.17e+01 bond pdb=" C ILE A 639 " pdb=" N PRO A 640 " ideal model delta sigma weight residual 1.330 1.386 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" N PRO A 640 " pdb=" CD PRO A 640 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CB ILE A1012 " pdb=" CG1 ILE A1012 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 6977 3.97 - 7.94: 201 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 2 Bond angle restraints: 7189 Sorted by residual: angle pdb=" N PRO C 22 " pdb=" CA PRO C 22 " pdb=" C PRO C 22 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 angle pdb=" C THR A1006 " pdb=" N PRO A1007 " pdb=" CA PRO A1007 " ideal model delta sigma weight residual 120.21 127.27 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C ARG C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta sigma weight residual 119.84 128.85 -9.01 1.25e+00 6.40e-01 5.20e+01 angle pdb=" C GLY C 43 " pdb=" N PRO C 44 " pdb=" CA PRO C 44 " ideal model delta sigma weight residual 120.21 126.84 -6.63 9.60e-01 1.09e+00 4.77e+01 angle pdb=" C THR A 823 " pdb=" N PRO A 824 " pdb=" CA PRO A 824 " ideal model delta sigma weight residual 119.78 126.72 -6.94 1.03e+00 9.43e-01 4.54e+01 ... (remaining 7184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 3129 32.24 - 64.48: 58 64.48 - 96.71: 7 96.71 - 128.95: 0 128.95 - 161.19: 1 Dihedral angle restraints: 3195 sinusoidal: 1367 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 710 " pdb=" CB CYS A 710 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" C3 PTY C 201 " pdb=" O11 PTY C 201 " pdb=" P1 PTY C 201 " pdb=" O12 PTY C 201 " ideal model delta sinusoidal sigma weight residual 300.23 139.04 161.19 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CD ARG C 20 " pdb=" NE ARG C 20 " pdb=" CZ ARG C 20 " pdb=" NH1 ARG C 20 " ideal model delta sinusoidal sigma weight residual 0.00 -36.88 36.88 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 3192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 519 0.095 - 0.191: 202 0.191 - 0.286: 32 0.286 - 0.381: 1 0.381 - 0.477: 3 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 639 " pdb=" CA ILE A 639 " pdb=" CG1 ILE A 639 " pdb=" CG2 ILE A 639 " both_signs ideal model delta sigma weight residual False 2.64 3.12 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2 NAG C 202 " pdb=" C1 NAG C 202 " pdb=" C3 NAG C 202 " pdb=" N2 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.49 -2.91 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C1 NAG C 202 " pdb=" ND2 ASN C 47 " pdb=" C2 NAG C 202 " pdb=" O5 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 754 not shown) Planarity restraints: 895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 20 " 0.647 9.50e-02 1.11e+02 2.90e-01 5.13e+01 pdb=" NE ARG C 20 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 20 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " -0.556 9.50e-02 1.11e+02 2.49e-01 3.79e+01 pdb=" NE ARG A1017 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 176 " 0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C HIS C 176 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS C 176 " 0.032 2.00e-02 2.50e+03 pdb=" OXT HIS C 176 " 0.032 2.00e-02 2.50e+03 ... (remaining 892 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1746 2.85 - 3.36: 5164 3.36 - 3.87: 9284 3.87 - 4.39: 10847 4.39 - 4.90: 17208 Nonbonded interactions: 44249 Sorted by model distance: nonbonded pdb=" NZ LYS A1015 " pdb=" OD1 ASP A1112 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.388 3.120 nonbonded pdb=" N ASP A 984 " pdb=" OD1 ASP A 984 " model vdw 2.407 3.120 nonbonded pdb=" NZ LYS A 827 " pdb=" OE2 GLU A 838 " model vdw 2.421 3.120 nonbonded pdb=" OD2 ASP A 572 " pdb=" NZ LYS A 642 " model vdw 2.444 3.120 ... (remaining 44244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.020 0.123 5358 Z= 1.057 Angle : 1.661 19.848 7202 Z= 1.122 Chirality : 0.098 0.477 757 Planarity : 0.015 0.290 894 Dihedral : 12.620 161.189 1988 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 2.86 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.34), residues: 584 helix: 1.44 (0.26), residues: 331 sheet: 0.62 (0.66), residues: 57 loop : 0.03 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 975 TYR 0.047 0.007 TYR C 154 PHE 0.025 0.005 PHE A 615 TRP 0.044 0.008 TRP C 133 HIS 0.007 0.002 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.01983 / 1.06 ( 5352) covalent geometry : angle 1.65854 / 1.12 ( 7189) SS BOND : bond 0.02808 / 1.71 ( 5) SS BOND : angle 2.95485 / 1.76 ( 10) hydrogen bonds : bond 0.17074 / 10.71 ( 331) hydrogen bonds : angle 7.09321 / 5.10 ( 948) link_NAG-ASN : bond 0.08466 / 4.46 ( 1) link_NAG-ASN : angle 2.47573 / 2.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7285 (mttt) cc_final: 0.6984 (mmtm) REVERT: A 1172 MET cc_start: 0.7568 (mmp) cc_final: 0.6645 (mmt) REVERT: C 75 GLN cc_start: 0.7771 (mt0) cc_final: 0.7215 (tt0) REVERT: C 160 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6412 (mt-10) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.0842 time to fit residues: 18.8638 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1174 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN A 611 ASN A 621 GLN A 716 ASN A 746 GLN A 749 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.218382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183100 restraints weight = 5914.679| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.87 r_work: 0.4108 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5358 Z= 0.169 Angle : 0.623 6.148 7202 Z= 0.345 Chirality : 0.043 0.204 757 Planarity : 0.004 0.042 894 Dihedral : 8.839 140.323 701 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.96 % Allowed : 9.11 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.22 (0.34), residues: 584 helix: 2.44 (0.26), residues: 348 sheet: -0.03 (0.55), residues: 72 loop : 0.12 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 96 TYR 0.023 0.002 TYR A1120 PHE 0.017 0.002 PHE A 655 TRP 0.015 0.002 TRP A 669 HIS 0.010 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 5352) covalent geometry : angle 0.61997 / 0.34 ( 7189) SS BOND : bond 0.00398 / 0.20 ( 5) SS BOND : angle 1.69160 / 1.00 ( 10) hydrogen bonds : bond 0.05036 / 3.10 ( 331) hydrogen bonds : angle 4.87140 / 3.50 ( 948) link_NAG-ASN : bond 0.00359 / 0.19 ( 1) link_NAG-ASN : angle 1.32371 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6731 (mttt) cc_final: 0.5820 (mmtm) REVERT: A 761 GLU cc_start: 0.6951 (tt0) cc_final: 0.6637 (mt-10) REVERT: A 840 PHE cc_start: 0.7852 (m-80) cc_final: 0.7304 (m-80) REVERT: A 882 LYS cc_start: 0.6586 (tttt) cc_final: 0.6237 (tptm) REVERT: A 883 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 1090 LYS cc_start: 0.7013 (tppt) cc_final: 0.5880 (pttp) REVERT: A 1172 MET cc_start: 0.7576 (mmp) cc_final: 0.6885 (mmt) REVERT: C 42 GLU cc_start: 0.7693 (tt0) cc_final: 0.7278 (tt0) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.0737 time to fit residues: 11.9838 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.208430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.174983 restraints weight = 5933.170| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.73 r_work: 0.4076 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5358 Z= 0.143 Angle : 0.555 8.561 7202 Z= 0.303 Chirality : 0.040 0.151 757 Planarity : 0.004 0.036 894 Dihedral : 7.417 96.876 701 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 12.50 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.23 (0.34), residues: 584 helix: 2.50 (0.26), residues: 353 sheet: -0.51 (0.54), residues: 73 loop : 0.19 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 96 TYR 0.016 0.002 TYR A 595 PHE 0.020 0.002 PHE A 655 TRP 0.014 0.001 TRP A 978 HIS 0.005 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5352) covalent geometry : angle 0.55270 / 0.30 ( 7189) SS BOND : bond 0.00378 / 0.20 ( 5) SS BOND : angle 1.22708 / 0.88 ( 10) hydrogen bonds : bond 0.04269 / 2.62 ( 331) hydrogen bonds : angle 4.51778 / 3.22 ( 948) link_NAG-ASN : bond 0.00141 / 0.07 ( 1) link_NAG-ASN : angle 1.65545 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6767 (mttt) cc_final: 0.6006 (mmtm) REVERT: A 714 ASN cc_start: 0.7330 (m110) cc_final: 0.7023 (m-40) REVERT: A 761 GLU cc_start: 0.7045 (tt0) cc_final: 0.6743 (mt-10) REVERT: A 840 PHE cc_start: 0.7903 (m-80) cc_final: 0.7487 (m-80) REVERT: A 882 LYS cc_start: 0.6589 (tttt) cc_final: 0.6239 (tptm) REVERT: A 915 TYR cc_start: 0.8410 (t80) cc_final: 0.7756 (t80) REVERT: A 1090 LYS cc_start: 0.6762 (tppt) cc_final: 0.5816 (pttp) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.0603 time to fit residues: 8.3497 Evaluate side-chains 87 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 ASN A 714 ASN A 756 HIS C 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.201486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167476 restraints weight = 5972.823| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.79 r_work: 0.3995 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5358 Z= 0.199 Angle : 0.608 11.101 7202 Z= 0.327 Chirality : 0.042 0.176 757 Planarity : 0.004 0.034 894 Dihedral : 6.941 64.066 701 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.21 % Allowed : 12.68 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.81 (0.34), residues: 584 helix: 2.19 (0.26), residues: 353 sheet: -0.80 (0.55), residues: 74 loop : 0.01 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 765 TYR 0.021 0.002 TYR A 595 PHE 0.026 0.002 PHE A 655 TRP 0.014 0.002 TRP A 978 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 5352) covalent geometry : angle 0.60444 / 0.33 ( 7189) SS BOND : bond 0.00506 / 0.27 ( 5) SS BOND : angle 1.57451 / 1.09 ( 10) hydrogen bonds : bond 0.04459 / 2.76 ( 331) hydrogen bonds : angle 4.65990 / 3.30 ( 948) link_NAG-ASN : bond 0.00046 / 0.02 ( 1) link_NAG-ASN : angle 1.82355 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6859 (mttt) cc_final: 0.6080 (mmtm) REVERT: A 761 GLU cc_start: 0.7137 (tt0) cc_final: 0.6801 (mt-10) REVERT: A 840 PHE cc_start: 0.8011 (m-80) cc_final: 0.7633 (m-80) REVERT: A 882 LYS cc_start: 0.6805 (tttt) cc_final: 0.6355 (tptm) REVERT: A 1090 LYS cc_start: 0.6594 (tppt) cc_final: 0.5652 (pttp) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.0656 time to fit residues: 9.1514 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.203532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169126 restraints weight = 6135.071| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.85 r_work: 0.4012 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5358 Z= 0.165 Angle : 0.591 9.739 7202 Z= 0.315 Chirality : 0.041 0.176 757 Planarity : 0.004 0.037 894 Dihedral : 6.799 54.832 701 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.32 % Allowed : 15.54 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.69 (0.34), residues: 584 helix: 2.15 (0.26), residues: 352 sheet: -0.92 (0.55), residues: 73 loop : -0.13 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.019 0.002 TYR A 595 PHE 0.023 0.002 PHE A 655 TRP 0.014 0.001 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5352) covalent geometry : angle 0.58803 / 0.31 ( 7189) SS BOND : bond 0.00417 / 0.21 ( 5) SS BOND : angle 1.42362 / 1.23 ( 10) hydrogen bonds : bond 0.04193 / 2.59 ( 331) hydrogen bonds : angle 4.50815 / 3.19 ( 948) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.71528 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6749 (mttt) cc_final: 0.6028 (mmtm) REVERT: A 761 GLU cc_start: 0.7065 (tt0) cc_final: 0.6777 (mt-10) REVERT: A 840 PHE cc_start: 0.7975 (m-80) cc_final: 0.7632 (m-80) REVERT: A 882 LYS cc_start: 0.6779 (tttt) cc_final: 0.6309 (tptm) REVERT: A 915 TYR cc_start: 0.8448 (t80) cc_final: 0.7721 (t80) REVERT: A 1090 LYS cc_start: 0.6602 (tppt) cc_final: 0.5617 (pttp) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 0.0703 time to fit residues: 9.0661 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 985 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 = 0.4513 r_free = 0.4513 target = 0.202848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.168753 restraints weight = 6091.386| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.79 r_work: 0.4015 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5358 Z= 0.161 Angle : 0.568 8.403 7202 Z= 0.307 Chirality : 0.041 0.170 757 Planarity : 0.004 0.040 894 Dihedral : 6.728 52.254 701 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.32 % Allowed : 15.89 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.71 (0.35), residues: 584 helix: 2.10 (0.26), residues: 354 sheet: -1.05 (0.56), residues: 73 loop : 0.11 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.019 0.002 TYR A 595 PHE 0.024 0.002 PHE C 123 TRP 0.017 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 5352) covalent geometry : angle 0.56452 / 0.31 ( 7189) SS BOND : bond 0.00391 / 0.20 ( 5) SS BOND : angle 1.45650 / 1.17 ( 10) hydrogen bonds : bond 0.04034 / 2.47 ( 331) hydrogen bonds : angle 4.42950 / 3.14 ( 948) link_NAG-ASN : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : angle 1.68594 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6674 (mttt) cc_final: 0.5934 (mmtm) REVERT: A 761 GLU cc_start: 0.7051 (tt0) cc_final: 0.6748 (mt-10) REVERT: A 840 PHE cc_start: 0.7962 (m-80) cc_final: 0.7641 (m-80) REVERT: A 882 LYS cc_start: 0.6792 (tttt) cc_final: 0.6198 (tppt) REVERT: A 1090 LYS cc_start: 0.6549 (tppt) cc_final: 0.5520 (pttt) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.0689 time to fit residues: 8.7223 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 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 = 0.4495 r_free = 0.4495 target = 0.200403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.166595 restraints weight = 6074.061| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.77 r_work: 0.3991 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5358 Z= 0.187 Angle : 0.596 8.013 7202 Z= 0.322 Chirality : 0.041 0.166 757 Planarity : 0.004 0.041 894 Dihedral : 6.823 57.479 701 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.37 (0.35), residues: 584 helix: 1.88 (0.26), residues: 354 sheet: -1.15 (0.57), residues: 74 loop : -0.16 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 765 TYR 0.018 0.002 TYR A 595 PHE 0.021 0.002 PHE C 123 TRP 0.015 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 5352) covalent geometry : angle 0.59306 / 0.32 ( 7189) SS BOND : bond 0.00382 / 0.20 ( 5) SS BOND : angle 1.41163 / 1.18 ( 10) hydrogen bonds : bond 0.04256 / 2.62 ( 331) hydrogen bonds : angle 4.53147 / 3.19 ( 948) link_NAG-ASN : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : angle 1.77327 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6677 (mttt) cc_final: 0.5941 (mmtm) REVERT: A 761 GLU cc_start: 0.7040 (tt0) cc_final: 0.6762 (mt-10) REVERT: A 840 PHE cc_start: 0.7977 (m-80) cc_final: 0.7670 (m-80) REVERT: A 882 LYS cc_start: 0.6846 (tttt) cc_final: 0.6227 (tppt) REVERT: A 891 LYS cc_start: 0.7500 (mttt) cc_final: 0.7274 (mmtt) REVERT: A 1090 LYS cc_start: 0.6624 (tppt) cc_final: 0.5552 (pttt) REVERT: C 42 GLU cc_start: 0.7675 (tp30) cc_final: 0.7319 (tp30) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.0805 time to fit residues: 10.2644 Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 157 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 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 = 0.4517 r_free = 0.4517 target = 0.203042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.169423 restraints weight = 5963.402| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.75 r_work: 0.4026 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5358 Z= 0.142 Angle : 0.546 7.329 7202 Z= 0.297 Chirality : 0.040 0.170 757 Planarity : 0.003 0.044 894 Dihedral : 6.647 59.905 701 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 18.04 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.35), residues: 584 helix: 2.13 (0.27), residues: 354 sheet: -1.19 (0.57), residues: 74 loop : -0.14 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 844 TYR 0.017 0.002 TYR A 595 PHE 0.020 0.002 PHE C 123 TRP 0.015 0.001 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5352) covalent geometry : angle 0.54365 / 0.30 ( 7189) SS BOND : bond 0.00319 / 0.16 ( 5) SS BOND : angle 1.16914 / 0.97 ( 10) hydrogen bonds : bond 0.03853 / 2.34 ( 331) hydrogen bonds : angle 4.35605 / 3.07 ( 948) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.62746 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6696 (mttt) cc_final: 0.6394 (mttm) REVERT: A 761 GLU cc_start: 0.7063 (tt0) cc_final: 0.6814 (mt-10) REVERT: A 840 PHE cc_start: 0.7931 (m-80) cc_final: 0.7636 (m-80) REVERT: A 882 LYS cc_start: 0.6785 (tttt) cc_final: 0.6209 (tppt) REVERT: A 915 TYR cc_start: 0.8516 (t80) cc_final: 0.7772 (t80) REVERT: A 1090 LYS cc_start: 0.6511 (tppt) cc_final: 0.5493 (pttt) REVERT: C 28 GLN cc_start: 0.7847 (tp40) cc_final: 0.7642 (tp40) REVERT: C 175 LYS cc_start: 0.8708 (mttp) cc_final: 0.8337 (mtmp) outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.0608 time to fit residues: 7.5624 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 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 = 0.4514 r_free = 0.4514 target = 0.202638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.168613 restraints weight = 6041.762| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.77 r_work: 0.4019 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5358 Z= 0.151 Angle : 0.558 7.315 7202 Z= 0.302 Chirality : 0.040 0.166 757 Planarity : 0.004 0.044 894 Dihedral : 6.650 60.732 701 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.32 % Allowed : 17.50 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.60 (0.35), residues: 584 helix: 2.12 (0.27), residues: 354 sheet: -0.97 (0.58), residues: 69 loop : -0.33 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 844 TYR 0.017 0.002 TYR A 595 PHE 0.020 0.002 PHE C 123 TRP 0.014 0.001 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 5352) covalent geometry : angle 0.55505 / 0.30 ( 7189) SS BOND : bond 0.00318 / 0.16 ( 5) SS BOND : angle 1.44499 / 1.09 ( 10) hydrogen bonds : bond 0.03854 / 2.34 ( 331) hydrogen bonds : angle 4.34199 / 3.05 ( 948) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.63056 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6670 (mttt) cc_final: 0.6366 (mttm) REVERT: A 761 GLU cc_start: 0.7046 (tt0) cc_final: 0.6802 (mt-10) REVERT: A 840 PHE cc_start: 0.7943 (m-80) cc_final: 0.7673 (m-80) REVERT: A 882 LYS cc_start: 0.6836 (tttt) cc_final: 0.6249 (tppt) REVERT: A 915 TYR cc_start: 0.8494 (t80) cc_final: 0.7820 (t80) REVERT: A 1090 LYS cc_start: 0.6396 (tppt) cc_final: 0.5446 (pttt) REVERT: C 28 GLN cc_start: 0.7820 (tp40) cc_final: 0.7563 (tp40) REVERT: C 175 LYS cc_start: 0.8682 (mttp) cc_final: 0.8405 (mtmp) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.0608 time to fit residues: 7.9340 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.199023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165067 restraints weight = 6026.338| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.76 r_work: 0.3975 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5358 Z= 0.205 Angle : 0.616 7.643 7202 Z= 0.333 Chirality : 0.042 0.183 757 Planarity : 0.004 0.044 894 Dihedral : 6.897 60.249 701 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.50 % Allowed : 17.68 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.20 (0.35), residues: 584 helix: 1.81 (0.26), residues: 354 sheet: -1.08 (0.59), residues: 69 loop : -0.54 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 844 TYR 0.017 0.002 TYR A1120 PHE 0.019 0.002 PHE C 123 TRP 0.015 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 5352) covalent geometry : angle 0.61273 / 0.33 ( 7189) SS BOND : bond 0.00461 / 0.25 ( 5) SS BOND : angle 1.59582 / 1.22 ( 10) hydrogen bonds : bond 0.04298 / 2.64 ( 331) hydrogen bonds : angle 4.60447 / 3.24 ( 948) link_NAG-ASN : bond 0.00046 / 0.02 ( 1) link_NAG-ASN : angle 1.85313 / 1.52 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 GLU cc_start: 0.6896 (tt0) cc_final: 0.6139 (mp0) REVERT: A 761 GLU cc_start: 0.7090 (tt0) cc_final: 0.6792 (mt-10) REVERT: A 840 PHE cc_start: 0.8073 (m-80) cc_final: 0.7781 (m-80) REVERT: A 882 LYS cc_start: 0.6803 (tttt) cc_final: 0.6229 (tppt) REVERT: A 1090 LYS cc_start: 0.6469 (tppt) cc_final: 0.5508 (pttt) REVERT: C 28 GLN cc_start: 0.7845 (tp40) cc_final: 0.7550 (tp40) REVERT: C 175 LYS cc_start: 0.8772 (mttp) cc_final: 0.8450 (mtmp) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.0684 time to fit residues: 8.4239 Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.200824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.166891 restraints weight = 6065.344| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.79 r_work: 0.4000 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5358 Z= 0.172 Angle : 0.591 7.409 7202 Z= 0.322 Chirality : 0.041 0.178 757 Planarity : 0.004 0.045 894 Dihedral : 6.822 60.379 701 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.32 % Allowed : 18.75 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.35), residues: 584 helix: 1.94 (0.26), residues: 354 sheet: -1.45 (0.58), residues: 74 loop : -0.39 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 844 TYR 0.016 0.002 TYR A 595 PHE 0.019 0.002 PHE C 123 TRP 0.015 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 5352) covalent geometry : angle 0.58826 / 0.32 ( 7189) SS BOND : bond 0.00330 / 0.17 ( 5) SS BOND : angle 1.41702 / 1.10 ( 10) hydrogen bonds : bond 0.04053 / 2.48 ( 331) hydrogen bonds : angle 4.48211 / 3.15 ( 948) link_NAG-ASN : bond 0.00056 / 0.03 ( 1) link_NAG-ASN : angle 1.74899 / 1.47 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1181.09 seconds wall clock time: 21 minutes 2.99 seconds (1262.99 seconds total)