Starting phenix.real_space_refine on Fri Aug 22 16:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_16416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_16416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_16416.map" model { file = "/net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_16416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c44_16416/08_2025/8c44_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-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.72, per 1000 atoms: 0.33 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: 0.51 Conformation dependent library (CDL) restraints added in 202.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.16 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: 0.97 Time building geometry restraints manager: 0.68 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: 3152 32.24 - 64.48: 62 64.48 - 96.71: 7 96.71 - 128.95: 0 128.95 - 161.19: 1 Dihedral angle restraints: 3222 sinusoidal: 1394 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 3219 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: 8.200 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.040 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 12.787 161.189 2015 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 aren 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 covalent geometry : bond 0.01983 ( 5352) covalent geometry : angle 1.65854 ( 7189) SS BOND : bond 0.02808 ( 5) SS BOND : angle 2.95485 ( 10) hydrogen bonds : bond 0.17074 ( 331) hydrogen bonds : angle 7.09321 ( 948) link_NAG-ASN : bond 0.08466 ( 1) link_NAG-ASN : angle 2.47573 ( 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 : 0.252 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: 0.1249 time to fit residues: 27.6581 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 : 0.218 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.210423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.176804 restraints weight = 5985.238| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.76 r_work: 0.4091 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3679 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= 0.167 Angle : 0.625 6.299 7202 Z= 0.349 Chirality : 0.042 0.166 757 Planarity : 0.005 0.043 894 Dihedral : 9.271 153.829 728 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.14 % Allowed : 9.11 % Favored : 88.75 % 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 aren not related in a simple way. whole: 2.24 (0.34), residues: 584 helix: 2.46 (0.26), residues: 348 sheet: -0.00 (0.54), 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 0.022 0.002 TYR A1120 PHE 0.018 0.002 PHE A 655 TRP 0.014 0.002 TRP A 978 HIS 0.010 0.002 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5352) covalent geometry : angle 0.62186 ( 7189) SS BOND : bond 0.00366 ( 5) SS BOND : angle 1.74837 ( 10) hydrogen bonds : bond 0.05236 ( 331) hydrogen bonds : angle 4.90328 ( 948) link_NAG-ASN : bond 0.00456 ( 1) link_NAG-ASN : angle 1.49695 ( 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: 12 poor density : 122 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 GLN cc_start: 0.6744 (pt0) cc_final: 0.5511 (mm-40) REVERT: A 552 LYS cc_start: 0.6721 (mttt) cc_final: 0.5834 (mmtm) REVERT: A 840 PHE cc_start: 0.7850 (m-80) cc_final: 0.7371 (m-80) REVERT: A 882 LYS cc_start: 0.6545 (tttt) cc_final: 0.6230 (tptm) REVERT: A 883 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 1090 LYS cc_start: 0.7088 (tppt) cc_final: 0.5940 (pttp) REVERT: A 1125 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8250 (mm-40) REVERT: A 1172 MET cc_start: 0.7631 (mmp) cc_final: 0.6919 (mmt) REVERT: C 42 GLU cc_start: 0.7621 (tt0) cc_final: 0.7214 (tt0) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.1101 time to fit residues: 17.4272 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 46 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN C 52 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.210338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177097 restraints weight = 5915.587| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.71 r_work: 0.4099 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5358 Z= 0.129 Angle : 0.531 6.954 7202 Z= 0.292 Chirality : 0.039 0.166 757 Planarity : 0.004 0.036 894 Dihedral : 8.089 123.180 728 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.96 % Allowed : 13.04 % Favored : 85.00 % 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 aren not related in a simple way. whole: 2.38 (0.34), residues: 584 helix: 2.60 (0.26), residues: 353 sheet: -0.37 (0.55), residues: 73 loop : 0.26 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.016 0.002 TYR A 595 PHE 0.021 0.002 PHE A 655 TRP 0.011 0.001 TRP A 669 HIS 0.005 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5352) covalent geometry : angle 0.52880 ( 7189) SS BOND : bond 0.00335 ( 5) SS BOND : angle 1.17662 ( 10) hydrogen bonds : bond 0.04111 ( 331) hydrogen bonds : angle 4.40111 ( 948) link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 1.60583 ( 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 118 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6779 (mttt) cc_final: 0.6023 (mmtm) REVERT: A 714 ASN cc_start: 0.7310 (m110) cc_final: 0.7004 (m-40) REVERT: A 761 GLU cc_start: 0.7100 (tt0) cc_final: 0.6841 (mt-10) REVERT: A 840 PHE cc_start: 0.7899 (m-80) cc_final: 0.7416 (m-80) REVERT: A 882 LYS cc_start: 0.6583 (tttt) cc_final: 0.6223 (tptm) REVERT: A 915 TYR cc_start: 0.8359 (t80) cc_final: 0.7675 (t80) REVERT: A 1090 LYS cc_start: 0.6646 (tppt) cc_final: 0.5686 (pttp) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.0836 time to fit residues: 12.1571 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 : 0.207 ------------------------------------------------------------------------------- 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 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 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 714 ASN A 756 HIS ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.207075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.173924 restraints weight = 5913.561| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.72 r_work: 0.4065 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5358 Z= 0.142 Angle : 0.539 8.678 7202 Z= 0.293 Chirality : 0.040 0.175 757 Planarity : 0.003 0.035 894 Dihedral : 7.453 99.749 728 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.50 % Allowed : 14.82 % Favored : 82.68 % 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 aren not related in a simple way. whole: 2.41 (0.35), residues: 584 helix: 2.55 (0.26), residues: 355 sheet: -0.53 (0.57), residues: 74 loop : 0.55 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.020 0.002 TYR A 595 PHE 0.028 0.002 PHE A 655 TRP 0.015 0.001 TRP A 978 HIS 0.004 0.001 HIS A1167 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5352) covalent geometry : angle 0.53654 ( 7189) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.25888 ( 10) hydrogen bonds : bond 0.03934 ( 331) hydrogen bonds : angle 4.37282 ( 948) link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.65021 ( 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 108 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6762 (mttt) cc_final: 0.6034 (mmtm) REVERT: A 761 GLU cc_start: 0.7045 (tt0) cc_final: 0.6803 (mt-10) REVERT: A 840 PHE cc_start: 0.7928 (m-80) cc_final: 0.7552 (m-80) REVERT: A 848 MET cc_start: 0.7588 (mmm) cc_final: 0.7304 (mmt) REVERT: A 882 LYS cc_start: 0.6714 (tttt) cc_final: 0.6277 (tptm) REVERT: A 915 TYR cc_start: 0.8417 (t80) cc_final: 0.7624 (t80) REVERT: A 1090 LYS cc_start: 0.6545 (tppt) cc_final: 0.5631 (pttp) REVERT: A 1197 ARG cc_start: 0.6281 (ttt180) cc_final: 0.6016 (ttp-170) REVERT: C 150 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7324 (mt0) outliers start: 14 outliers final: 7 residues processed: 103 average time/residue: 0.0860 time to fit residues: 11.4594 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.0020 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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 = 0.4529 r_free = 0.4529 target = 0.204826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.170130 restraints weight = 6127.494| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.87 r_work: 0.4021 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5358 Z= 0.168 Angle : 0.608 11.011 7202 Z= 0.324 Chirality : 0.041 0.185 757 Planarity : 0.004 0.038 894 Dihedral : 7.400 88.107 728 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.86 % Allowed : 14.82 % Favored : 82.32 % 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 aren not related in a simple way. whole: 2.13 (0.35), residues: 584 helix: 2.39 (0.26), residues: 354 sheet: -0.89 (0.56), residues: 74 loop : 0.43 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.020 0.002 TYR A 595 PHE 0.023 0.002 PHE A 655 TRP 0.015 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5352) covalent geometry : angle 0.59740 ( 7189) SS BOND : bond 0.00380 ( 5) SS BOND : angle 3.02204 ( 10) hydrogen bonds : bond 0.04211 ( 331) hydrogen bonds : angle 4.50985 ( 948) link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.72109 ( 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 108 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6782 (mttt) cc_final: 0.6055 (mmtm) REVERT: A 761 GLU cc_start: 0.7081 (tt0) cc_final: 0.6781 (mt-10) REVERT: A 840 PHE cc_start: 0.7970 (m-80) cc_final: 0.7620 (m-80) REVERT: A 882 LYS cc_start: 0.6758 (tttt) cc_final: 0.6289 (tptm) REVERT: A 1090 LYS cc_start: 0.6611 (tppt) cc_final: 0.5648 (pttt) REVERT: A 1197 ARG cc_start: 0.6413 (ttt180) cc_final: 0.6114 (ttp-170) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.0817 time to fit residues: 10.9116 Evaluate side-chains 87 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 613 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 741 VAL 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 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.200957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.166385 restraints weight = 6088.861| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.85 r_work: 0.3980 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5358 Z= 0.202 Angle : 0.638 9.320 7202 Z= 0.341 Chirality : 0.042 0.175 757 Planarity : 0.004 0.038 894 Dihedral : 7.354 72.215 728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.68 % Allowed : 16.43 % Favored : 80.89 % 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 aren not related in a simple way. whole: 1.57 (0.34), residues: 584 helix: 2.04 (0.26), residues: 352 sheet: -1.23 (0.56), residues: 74 loop : 0.05 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 765 TYR 0.021 0.002 TYR A 595 PHE 0.022 0.003 PHE A 662 TRP 0.018 0.002 TRP A 978 HIS 0.003 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 5352) covalent geometry : angle 0.62961 ( 7189) SS BOND : bond 0.00473 ( 5) SS BOND : angle 2.68197 ( 10) hydrogen bonds : bond 0.04432 ( 331) hydrogen bonds : angle 4.68958 ( 948) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.89124 ( 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 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6696 (mttt) cc_final: 0.5991 (mmtm) REVERT: A 761 GLU cc_start: 0.7084 (tt0) cc_final: 0.6787 (mt-10) REVERT: A 840 PHE cc_start: 0.8031 (m-80) cc_final: 0.7689 (m-80) REVERT: A 882 LYS cc_start: 0.6853 (tttt) cc_final: 0.6351 (tptm) REVERT: A 1090 LYS cc_start: 0.6630 (tppt) cc_final: 0.5571 (pttt) REVERT: A 1113 LYS cc_start: 0.8451 (mttt) cc_final: 0.8233 (tptp) outliers start: 15 outliers final: 9 residues processed: 94 average time/residue: 0.0671 time to fit residues: 8.0194 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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 = 0.202896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168930 restraints weight = 6075.103| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.80 r_work: 0.4022 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5358 Z= 0.165 Angle : 0.596 8.584 7202 Z= 0.319 Chirality : 0.040 0.182 757 Planarity : 0.004 0.042 894 Dihedral : 7.086 64.877 728 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 17.32 % Favored : 80.54 % 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 aren not related in a simple way. whole: 1.66 (0.35), residues: 584 helix: 2.09 (0.26), residues: 354 sheet: -1.41 (0.55), residues: 74 loop : 0.23 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 844 TYR 0.018 0.002 TYR A 595 PHE 0.020 0.002 PHE A 655 TRP 0.015 0.002 TRP A 978 HIS 0.003 0.001 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5352) covalent geometry : angle 0.58722 ( 7189) SS BOND : bond 0.00425 ( 5) SS BOND : angle 2.69511 ( 10) hydrogen bonds : bond 0.04087 ( 331) hydrogen bonds : angle 4.56973 ( 948) link_NAG-ASN : bond 0.00014 ( 1) link_NAG-ASN : angle 1.75896 ( 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 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6586 (mttt) cc_final: 0.6349 (mttp) REVERT: A 761 GLU cc_start: 0.7079 (tt0) cc_final: 0.6790 (mt-10) REVERT: A 840 PHE cc_start: 0.7959 (m-80) cc_final: 0.7659 (m-80) REVERT: A 882 LYS cc_start: 0.6780 (tttt) cc_final: 0.6158 (tppt) REVERT: A 1090 LYS cc_start: 0.6550 (tppt) cc_final: 0.5552 (pttt) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.0667 time to fit residues: 7.7401 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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 = 0.4502 r_free = 0.4502 target = 0.205375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168709 restraints weight = 5996.726| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.94 r_work: 0.3963 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5358 Z= 0.253 Angle : 0.679 8.673 7202 Z= 0.362 Chirality : 0.044 0.200 757 Planarity : 0.004 0.041 894 Dihedral : 7.509 62.105 728 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 17.86 % Favored : 79.64 % 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 aren not related in a simple way. whole: 1.02 (0.34), residues: 584 helix: 1.62 (0.26), residues: 352 sheet: -1.44 (0.56), residues: 73 loop : -0.25 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.018 0.002 TYR A 595 PHE 0.019 0.003 PHE A 662 TRP 0.016 0.002 TRP A 669 HIS 0.004 0.001 HIS A 702 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 5352) covalent geometry : angle 0.66921 ( 7189) SS BOND : bond 0.00558 ( 5) SS BOND : angle 2.94955 ( 10) hydrogen bonds : bond 0.04714 ( 331) hydrogen bonds : angle 4.83133 ( 948) link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 2.11544 ( 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 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6741 (mttt) cc_final: 0.6498 (mttp) REVERT: A 705 GLU cc_start: 0.6795 (tt0) cc_final: 0.6106 (mp0) REVERT: A 882 LYS cc_start: 0.6820 (tttt) cc_final: 0.6200 (tppt) REVERT: A 891 LYS cc_start: 0.7563 (mttt) cc_final: 0.7361 (mmtt) REVERT: A 1090 LYS cc_start: 0.6531 (tppt) cc_final: 0.5475 (pttt) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.0762 time to fit residues: 8.5071 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 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 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 69 LEU 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: 0.0980 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 chunk 25 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 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 = 0.4547 r_free = 0.4547 target = 0.205893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.172579 restraints weight = 6020.062| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.76 r_work: 0.4064 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5358 Z= 0.124 Angle : 0.568 8.496 7202 Z= 0.305 Chirality : 0.039 0.159 757 Planarity : 0.004 0.046 894 Dihedral : 6.904 62.345 728 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.79 % Allowed : 18.93 % Favored : 79.29 % 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 aren not related in a simple way. whole: 1.65 (0.35), residues: 584 helix: 2.19 (0.27), residues: 355 sheet: -1.56 (0.56), residues: 74 loop : -0.02 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 844 TYR 0.016 0.001 TYR A 595 PHE 0.021 0.002 PHE A 655 TRP 0.016 0.002 TRP A 979 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5352) covalent geometry : angle 0.56101 ( 7189) SS BOND : bond 0.00316 ( 5) SS BOND : angle 2.22288 ( 10) hydrogen bonds : bond 0.03733 ( 331) hydrogen bonds : angle 4.41025 ( 948) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 1.63763 ( 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 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6549 (mttt) cc_final: 0.6293 (mttm) REVERT: A 662 PHE cc_start: 0.7582 (m-10) cc_final: 0.7207 (m-80) REVERT: A 840 PHE cc_start: 0.7688 (m-80) cc_final: 0.7485 (m-80) REVERT: A 882 LYS cc_start: 0.6764 (tttt) cc_final: 0.6159 (tppt) REVERT: A 915 TYR cc_start: 0.8500 (t80) cc_final: 0.7753 (t80) REVERT: A 1090 LYS cc_start: 0.6539 (tppt) cc_final: 0.5533 (pttt) REVERT: A 1125 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8214 (tp40) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.0758 time to fit residues: 8.5416 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 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 = 0.4522 r_free = 0.4522 target = 0.203178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.169140 restraints weight = 6023.240| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.77 r_work: 0.4026 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5926 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= 0.160 Angle : 0.588 7.956 7202 Z= 0.314 Chirality : 0.040 0.168 757 Planarity : 0.004 0.044 894 Dihedral : 6.902 61.823 728 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.25 % Allowed : 19.82 % 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 aren not related in a simple way. whole: 1.59 (0.35), residues: 584 helix: 2.12 (0.27), residues: 354 sheet: -1.24 (0.58), residues: 69 loop : -0.21 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.016 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 covalent geometry : bond 0.00374 ( 5352) covalent geometry : angle 0.58149 ( 7189) SS BOND : bond 0.00369 ( 5) SS BOND : angle 2.21456 ( 10) hydrogen bonds : bond 0.03960 ( 331) hydrogen bonds : angle 4.49726 ( 948) link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.70182 ( 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 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6741 (mttt) cc_final: 0.6441 (mttm) REVERT: A 662 PHE cc_start: 0.7665 (m-10) cc_final: 0.7288 (m-80) REVERT: A 840 PHE cc_start: 0.7784 (m-80) cc_final: 0.7551 (m-80) REVERT: A 882 LYS cc_start: 0.6816 (tttt) cc_final: 0.6209 (tppt) REVERT: A 1090 LYS cc_start: 0.6502 (tppt) cc_final: 0.5563 (pttt) REVERT: A 1125 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8229 (tp40) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.0797 time to fit residues: 8.5102 Evaluate side-chains 81 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 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 = 0.4523 r_free = 0.4523 target = 0.202962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.168904 restraints weight = 6089.488| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.79 r_work: 0.4028 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5358 Z= 0.165 Angle : 0.600 7.851 7202 Z= 0.319 Chirality : 0.041 0.174 757 Planarity : 0.004 0.076 894 Dihedral : 6.915 63.043 728 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.61 % Allowed : 19.46 % 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 aren not related in a simple way. whole: 1.53 (0.35), residues: 584 helix: 2.08 (0.27), residues: 354 sheet: -1.24 (0.58), residues: 69 loop : -0.28 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 844 TYR 0.016 0.002 TYR A 595 PHE 0.018 0.002 PHE A 655 TRP 0.015 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5352) covalent geometry : angle 0.59428 ( 7189) SS BOND : bond 0.00363 ( 5) SS BOND : angle 2.19645 ( 10) hydrogen bonds : bond 0.03982 ( 331) hydrogen bonds : angle 4.50774 ( 948) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.69791 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1407.65 seconds wall clock time: 24 minutes 51.09 seconds (1491.09 seconds total)